I've recently setup Mach3's Charge Pump feature and do not have "charge pump on in estop" checked and get the following behavior that I want.
Mach3 not running, no charge pump 12.5Khz output on BOB
Mach3 running, Reset flashing, no 12.5Khz output
Mach3 running, Reset clicked, solid Reset button, got 12.5Kz output on BOB
Mach3 running, Reset clicked, Reset button flashing, no 12.5Khz output on BOB
Hit eStop , Reset button flashes, no 12.5Khz output on BOB
I noticed that the Gecko G540 drive's charge pump feature expects a 10Khz input on pin 16 of the DB25 port. Mach3 puts out a 12.5Khz Charge Pump square wave. You might check with GeckoDrive and ask them what the frequency "slack" is on the G540.