Ok, being the dummy that I am, it took me a while to understand about the filtering. When I looked at it, there was no filtering at all (0), I bumped the filtering up to 1000 and tried again. Same result. Bumped it to 2000. Same result. I am not sure how high I should go. The log file for these two attempts is below if that tells anyone anything usefull.
2019-07-13 13:50:10.480 - Loggging Enabled.
2019-07-13 13:50:22.216 - API: mcCntlEnable(true) called.
2019-07-13 13:50:22.217 - Signal id 1019, (Enable #1), changed from LOW to HIGH.
2019-07-13 13:50:22.217 - Signal id 1021, (Enable #3), changed from LOW to HIGH.
2019-07-13 13:50:22.217 - Signal id 1020, (Enable #2), changed from LOW to HIGH.
2019-07-13 13:50:22.218 - Signal id 1120, (Machine Enabled), changed from LOW to HIGH.
2019-07-13 13:50:30.719 - API: mcCntlGcodeExecute() called. (G91 G31 Z -5.25F5)
2019-07-13 13:50:30.919 - Attempt transition from "Idle" on event "MDI Start" Controller.cpp:1811
2019-07-13 13:50:30.919 - S_IDLE_on_exit
2019-07-13 13:50:30.919 - ACTION_start_mdi
2019-07-13 13:50:30.919 - S_MDI_RUNNING_on_entry
2019-07-13 13:50:30.919 - S_MDI_RUNNING2_on_entry
2019-07-13 13:50:30.920 - Signal id 1114, (Gcode Running), changed from LOW to HIGH.
2019-07-13 13:50:30.936 - Attempt transition from "MDI Running" on event "Probe" RunCanon.cpp:497
2019-07-13 13:50:30.936 - S_MDI_RUNNING2_on_exit
2019-07-13 13:50:30.936 - Signal id 1114, (Gcode Running), changed from HIGH to LOW.
2019-07-13 13:50:30.936 - ACTION_start_probe
2019-07-13 13:50:30.937 - >>>>> ESS Probe 0, Starting.
2019-07-13 13:50:30.938 - S_MDI_PROBING_on_entry
2019-07-13 13:50:30.938 - Probing: Waiting on exit event... RunCanon.cpp:236
2019-07-13 13:50:30.938 - Controller::RunCanonBuffer called AddStopReportRequest() RunCanon.cpp:76
2019-07-13 13:50:30.938 - Requesting a stopped report for axis 0 motors.
2019-07-13 13:50:30.938 - Requesting a stopped report for motor 0.
2019-07-13 13:50:30.938 - Requesting a stopped report for axis 1 motors.
2019-07-13 13:50:30.938 - Requesting a stopped report for motor 1.
2019-07-13 13:50:30.938 - Requesting a stopped report for motor 3.
2019-07-13 13:50:30.938 - Requesting a stopped report for axis 2 motors.
2019-07-13 13:50:30.938 - Requesting a stopped report for motor 2.
2019-07-13 13:50:30.939 - Waiting on SetStill...
2019-07-13 13:50:30.960 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 0
2019-07-13 13:50:30.960 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 1
2019-07-13 13:50:30.960 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 2
2019-07-13 13:50:30.960 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 3
2019-07-13 13:50:30.960 - >>>>ESS: Switching from NORMAL to PROBE state for Probe 0
2019-07-13 13:50:31.510 - -----ESS: Checking for Probe0 Strike, none yet...
2019-07-13 13:50:32.060 - -----ESS: Checking for Probe0 Strike, none yet...
2019-07-13 13:50:32.360 - Signal id 161, (PROBE), changed from LOW to HIGH.
2019-07-13 13:50:32.360 - -----ESS: Mach ACKs Probe0 input signal ON!
2019-07-13 13:50:32.361 - API: mcMotionSetProbePos() called. motor 0 position 0.0000
2019-07-13 13:50:32.361 - API: mcMotionSetProbePos() called. motor 1 position 0.0000
2019-07-13 13:50:32.361 - API: mcMotionSetProbePos() called. motor 2 position -54.0000
2019-07-13 13:50:32.361 - API: mcMotionSetProbePos() called. motor 3 position 0.0000
2019-07-13 13:50:32.361 - API: mcMotionSetProbePos() called. motor 4 position 0.0000
2019-07-13 13:50:32.361 - API: mcMotionSetProbePos() called. motor 5 position 0.0000
2019-07-13 13:50:32.361 - ^^^^^^ ESS: Success! Probe0 Strike. Switching from PROBING to PROBING_CLEANUP state.
2019-07-13 13:50:32.410 - ^^^^^^ ESS Probe0 Finished: The device is still and the buffer is empty.
2019-07-13 13:50:32.410 - API: mcMotionClearPlanner() called.
2019-07-13 13:50:32.410 - API: mcMotionSetProbeComplete() called.
2019-07-13 13:50:32.410 - Recording latched probe positions.
2019-07-13 13:50:32.411 - Attempt transition from "Probing" on event "Probe Complete" MachAPI.cpp:1348
2019-07-13 13:50:32.411 - S_MDI_PROBING_on_exit
2019-07-13 13:50:32.411 - ACTION_stop_probe
2019-07-13 13:50:32.411 - >>>>> ESS Probe 0, Done
2019-07-13 13:50:32.413 - S_MDI_RUNNING2_on_entry
2019-07-13 13:50:32.413 - Signal id 1114, (Gcode Running), changed from LOW to HIGH.
2019-07-13 13:50:32.415 - SyncPosition()! Clearing planner.
2019-07-13 13:50:32.415 - .^^^^^ESS: Switching from PROBING_CLEANUP to NORMAL state.
2019-07-13 13:50:32.415 -
2019-07-13 13:50:32.415 - Waiting on SetStill is Done!
2019-07-13 13:50:32.415 - Probing: Exiting hold because of probe strike. GcodeExec.cpp:1272
2019-07-13 13:50:32.535 - Attempt transition from "MDI Running" on event "Stop" GcodeExec.cpp:1099
2019-07-13 13:50:32.535 - S_MDI_RUNNING2_on_exit
2019-07-13 13:50:32.535 - Signal id 1114, (Gcode Running), changed from HIGH to LOW.
2019-07-13 13:50:32.535 - S_MDI_RUNNING_on_exit
2019-07-13 13:50:32.535 - ACTION_stop
2019-07-13 13:50:32.560 - Signal id 161, (PROBE), changed from HIGH to LOW.
2019-07-13 13:50:32.562 - S_IDLE_on_entry
2019-07-13 13:50:32.562 - -----ESS: Mach ACKs Probe0 input signal OFF.
2019-07-13 13:50:32.623 - API: mcCntlGcodeExecute() called. (G 91
F 5)
2019-07-13 13:50:32.823 - Attempt transition from "Idle" on event "MDI Start" Controller.cpp:1811
2019-07-13 13:50:32.823 - S_IDLE_on_exit
2019-07-13 13:50:32.823 - ACTION_start_mdi
2019-07-13 13:50:32.823 - S_MDI_RUNNING_on_entry
2019-07-13 13:50:32.823 - S_MDI_RUNNING2_on_entry
2019-07-13 13:50:32.824 - Signal id 1114, (Gcode Running), changed from LOW to HIGH.
2019-07-13 13:50:32.846 - API: mcCntlEStop() called.
2019-07-13 13:50:32.846 - API: mcCntlEnable(false) called.
2019-07-13 13:50:32.846 - API: mcCntlCycleStop() called.
2019-07-13 13:50:32.847 - Signal id 1019, (Enable #1), changed from HIGH to LOW.
2019-07-13 13:50:32.847 - Signal id 1021, (Enable #3), changed from HIGH to LOW.
2019-07-13 13:50:32.847 - Attempt transition from "MDI Running" on event "Stop" MachAPI.cpp:2678
2019-07-13 13:50:32.847 - S_MDI_RUNNING2_on_exit
2019-07-13 13:50:32.847 - Signal id 1114, (Gcode Running), changed from HIGH to LOW.
2019-07-13 13:50:32.847 - Signal id 1020, (Enable #2), changed from HIGH to LOW.
2019-07-13 13:50:32.848 - Attempt transition from "MDI Running" on event "Stop" Controller.cpp:4535
2019-07-13 13:50:32.848 - S_MDI_RUNNING_on_exit
2019-07-13 13:50:32.848 - Signal id 1120, (Machine Enabled), changed from HIGH to LOW.
2019-07-13 13:50:32.848 - ACTION_stop
2019-07-13 13:50:32.848 -
2019-07-13 13:50:32.848 - $$$ ESS: Mach4 was Disabled - Force Output Stop Sates Now
2019-07-13 13:50:32.848 - !!! ESS: Stop Event IGNORING command to turn OFF DISABLED output Port1-Pin14 - Spindle ON Relay
2019-07-13 13:50:32.848 - $$$ ESS: Finished processing the Stop Event
2019-07-13 13:50:32.848 -
2019-07-13 13:50:32.872 - S_IDLE_on_entry
2019-07-13 13:50:32.937 - Attempt transition from "Idle" on event "Stop" GcodeExec.cpp:1099
2019-07-13 13:50:32.937 - Can't transition from "Idle" on event "Stop"
2019-07-13 13:54:07.881 - -----ESS: Switching from NORMAL to CONFIG state
2019-07-13 13:54:40.889 - ESS Called its Reconfigure() function
2019-07-13 13:54:40.911 - ESS: Switching from CONFIG to NORMAL state
2019-07-13 13:54:46.193 - API: mcCntlEnable(true) called.
2019-07-13 13:54:46.193 - Signal id 1019, (Enable #1), changed from LOW to HIGH.
2019-07-13 13:54:46.194 - Signal id 1021, (Enable #3), changed from LOW to HIGH.
2019-07-13 13:54:46.194 - Signal id 1020, (Enable #2), changed from LOW to HIGH.
2019-07-13 13:54:46.194 - Signal id 1120, (Machine Enabled), changed from LOW to HIGH.
2019-07-13 13:54:57.194 - API: mcJogVelocityStart() called. Axis 2, dir = 1
2019-07-13 13:54:57.194 - Attempt transition from "Idle" on event "Jog" Axis.cpp:632
2019-07-13 13:54:57.194 - S_IDLE_on_exit
2019-07-13 13:54:57.194 - ACTION_start_jogging
2019-07-13 13:54:57.194 - S_JOGGING_on_entry
2019-07-13 13:54:58.362 - API: mcJogVelocityStop() called. Axis 2
2019-07-13 13:54:58.915 - Requesting a stopped report for axis 2 motors. Axis.cpp:806
2019-07-13 13:54:58.915 - Requesting a stopped report for motor 2.
2019-07-13 13:54:58.915 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 2
2019-07-13 13:54:59.114 - All motors marked as still.
2019-07-13 13:54:59.114 - Main planner updated from last mcMotionSetPos().
2019-07-13 13:54:59.114 - Attempt transition from "Jogging" on event "Stop Jog" Controller.cpp:1076
2019-07-13 13:54:59.115 - S_JOGGING_on_exit
2019-07-13 13:54:59.115 - S_FILE_RUNNING_stop_jogging
2019-07-13 13:54:59.115 - S_IDLE_on_entry
2019-07-13 13:54:59.115 - Signal id 1127, (Jog Enabled), changed from LOW to HIGH.
2019-07-13 13:54:59.115 - -----ESS: Motor 2 Still
2019-07-13 13:55:07.277 - API: mcCntlGcodeExecute() called. (G91 G31 Z -5.25F5)
2019-07-13 13:55:07.477 - Attempt transition from "Idle" on event "MDI Start" Controller.cpp:1811
2019-07-13 13:55:07.477 - Signal id 1127, (Jog Enabled), changed from HIGH to LOW.
2019-07-13 13:55:07.477 - S_IDLE_on_exit
2019-07-13 13:55:07.477 - ACTION_start_mdi
2019-07-13 13:55:07.477 - S_MDI_RUNNING_on_entry
2019-07-13 13:55:07.477 - S_MDI_RUNNING2_on_entry
2019-07-13 13:55:07.478 - Signal id 1114, (Gcode Running), changed from LOW to HIGH.
2019-07-13 13:55:07.493 - Attempt transition from "MDI Running" on event "Probe" RunCanon.cpp:497
2019-07-13 13:55:07.494 - S_MDI_RUNNING2_on_exit
2019-07-13 13:55:07.494 - Signal id 1114, (Gcode Running), changed from HIGH to LOW.
2019-07-13 13:55:07.494 - ACTION_start_probe
2019-07-13 13:55:07.494 - >>>>> ESS Probe 0, Starting.
2019-07-13 13:55:07.496 - S_MDI_PROBING_on_entry
2019-07-13 13:55:07.496 - Probing: Waiting on exit event... RunCanon.cpp:236
2019-07-13 13:55:07.496 - Controller::RunCanonBuffer called AddStopReportRequest() RunCanon.cpp:76
2019-07-13 13:55:07.496 - Requesting a stopped report for axis 0 motors.
2019-07-13 13:55:07.496 - Requesting a stopped report for motor 0.
2019-07-13 13:55:07.496 - Requesting a stopped report for axis 1 motors.
2019-07-13 13:55:07.496 - Requesting a stopped report for motor 1.
2019-07-13 13:55:07.497 - Requesting a stopped report for motor 3.
2019-07-13 13:55:07.497 - Requesting a stopped report for axis 2 motors.
2019-07-13 13:55:07.497 - Requesting a stopped report for motor 2.
2019-07-13 13:55:07.497 - Waiting on SetStill...
2019-07-13 13:55:07.516 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 0
2019-07-13 13:55:07.516 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 1
2019-07-13 13:55:07.516 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 2
2019-07-13 13:55:07.516 - -----ESS: Mach requested MSG_REPORT_MOTOR_STOP Motor 3
2019-07-13 13:55:07.516 - >>>>ESS: Switching from NORMAL to PROBE state for Probe 0
2019-07-13 13:55:08.065 - -----ESS: Checking for Probe0 Strike, none yet...
2019-07-13 13:55:08.615 - -----ESS: Checking for Probe0 Strike, none yet...
2019-07-13 13:55:08.668 - Signal id 161, (PROBE), changed from LOW to HIGH.
2019-07-13 13:55:08.668 - API: mcMotionSetProbePos() called. motor 0 position 0.0000
2019-07-13 13:55:08.669 - API: mcMotionSetProbePos() called. motor 1 position 0.0000
2019-07-13 13:55:08.669 - API: mcMotionSetProbePos() called. motor 2 position 3199.0000
2019-07-13 13:55:08.669 - API: mcMotionSetProbePos() called. motor 3 position 0.0000
2019-07-13 13:55:08.669 - API: mcMotionSetProbePos() called. motor 4 position 0.0000
2019-07-13 13:55:08.669 - API: mcMotionSetProbePos() called. motor 5 position 0.0000
2019-07-13 13:55:08.669 - ^^^^^^ ESS: Success! Probe0 Strike. Switching from PROBING to PROBING_CLEANUP state.
2019-07-13 13:55:08.669 - -----ESS: Mach ACKs Probe0 input signal ON!
2019-07-13 13:55:08.718 - ^^^^^^ ESS Probe0 Finished: The device is still and the buffer is empty.
2019-07-13 13:55:08.718 - API: mcMotionClearPlanner() called.
2019-07-13 13:55:08.718 - API: mcMotionSetProbeComplete() called.
2019-07-13 13:55:08.718 - Recording latched probe positions.
2019-07-13 13:55:08.718 - Attempt transition from "Probing" on event "Probe Complete" MachAPI.cpp:1348
2019-07-13 13:55:08.718 - S_MDI_PROBING_on_exit
2019-07-13 13:55:08.719 - ACTION_stop_probe
2019-07-13 13:55:08.719 - >>>>> ESS Probe 0, Done
2019-07-13 13:55:08.721 - S_MDI_RUNNING2_on_entry
2019-07-13 13:55:08.721 - Signal id 1114, (Gcode Running), changed from LOW to HIGH.
2019-07-13 13:55:08.723 - SyncPosition()! Clearing planner.
2019-07-13 13:55:08.723 - .^^^^^ESS: Switching from PROBING_CLEANUP to NORMAL state.
2019-07-13 13:55:08.723 -
2019-07-13 13:55:08.723 - Waiting on SetStill is Done!
2019-07-13 13:55:08.723 - Probing: Exiting hold because of probe strike. GcodeExec.cpp:1272
2019-07-13 13:55:08.793 - Signal id 161, (PROBE), changed from HIGH to LOW.
2019-07-13 13:55:08.794 - -----ESS: Mach ACKs Probe0 input signal OFF.
2019-07-13 13:55:08.843 - Attempt transition from "MDI Running" on event "Stop" GcodeExec.cpp:1099
2019-07-13 13:55:08.843 - S_MDI_RUNNING2_on_exit
2019-07-13 13:55:08.843 - Signal id 1114, (Gcode Running), changed from HIGH to LOW.
2019-07-13 13:55:08.843 - S_MDI_RUNNING_on_exit
2019-07-13 13:55:08.843 - ACTION_stop
2019-07-13 13:55:08.869 - S_IDLE_on_entry
2019-07-13 13:55:08.870 - API: mcCntlGcodeExecute() called. (G 91
F 5)
2019-07-13 13:55:09.070 - Attempt transition from "Idle" on event "MDI Start" Controller.cpp:1811
2019-07-13 13:55:09.070 - S_IDLE_on_exit
2019-07-13 13:55:09.070 - ACTION_start_mdi
2019-07-13 13:55:09.070 - S_MDI_RUNNING_on_entry
2019-07-13 13:55:09.070 - S_MDI_RUNNING2_on_entry
2019-07-13 13:55:09.071 - Signal id 1114, (Gcode Running), changed from LOW to HIGH.
2019-07-13 13:55:09.093 - API: mcCntlEStop() called.
2019-07-13 13:55:09.093 - API: mcCntlEnable(false) called.
2019-07-13 13:55:09.093 - API: mcCntlCycleStop() called.
2019-07-13 13:55:09.093 - Signal id 1019, (Enable #1), changed from HIGH to LOW.
2019-07-13 13:55:09.094 - Signal id 1021, (Enable #3), changed from HIGH to LOW.
2019-07-13 13:55:09.094 - Signal id 1020, (Enable #2), changed from HIGH to LOW.
2019-07-13 13:55:09.094 - Attempt transition from "MDI Running" on event "Stop" Controller.cpp:4535
2019-07-13 13:55:09.094 - S_MDI_RUNNING2_on_exit
2019-07-13 13:55:09.094 - Signal id 1114, (Gcode Running), changed from HIGH to LOW.
2019-07-13 13:55:09.094 - S_MDI_RUNNING_on_exit
2019-07-13 13:55:09.094 - ACTION_stop
2019-07-13 13:55:09.095 -
2019-07-13 13:55:09.095 - $$$ ESS: Mach4 had a Cycle Stop - Force Output Stop Sates Now
2019-07-13 13:55:09.095 - Attempt transition from "MDI Running" on event "Stop" MachAPI.cpp:2678
2019-07-13 13:55:09.095 - !!! ESS: Stop Event IGNORING command to turn OFF DISABLED output Port1-Pin14 - Spindle ON Relay
2019-07-13 13:55:09.095 - $$$ ESS: Finished processing the Stop Event
2019-07-13 13:55:09.096 -
2019-07-13 13:55:09.120 - S_IDLE_on_entry
2019-07-13 13:55:09.120 - Signal id 1120, (Machine Enabled), changed from HIGH to LOW.