Understand that, Dave. I like having it that way too. I've set up an M6Start macro that positions the spindle to a user defined location using the "Tool Change Location" DROs in the settings page and then prompts for the tool to be changed. It waits for the tool to be changed and acknowledged then asks for an auto tool zero (with OK or Cancel buttons) and if auto is selected it moves to the Z location specified as above (the tool change is done at SafeZ if defined or 0 if not) and begins the probe move. Cancel lets you do it manually. Then press "Cycle Start" to run the M6End macro which positions the tool at the location it was when the M6 command was triggered in the program and continues on.
My advice to use a "do nothing" M6 macro is for troubleshooting to determine if it's a macro problem or a bug in the program. I'll have another look at mine to see if jogging causes problems in the manual operation of the macro.
Stephen "Highspeed" Kruse
EDIT: Reading through this post again, I just noticed that you did try blank macros already. I'll have a go at it later today and see how it works out for me. What components are you using for your electronics? (Breakout board, motion controller, stepper drivers, etc.)