OK, I just mentioned to spindle in passing as it is pulse width sensitive.

Just download the latest version to check and it's impossible to have different pulse widths setup for different axis.

It doesn't matter if you have 15 power supply's or driver, you only have one copy of Mach.

The pulse width setting I'm talking about is in Config > Motor tuning. Step pulse which is slightly to the right at the bottom of the screen. Any alterations HAS to have the save setting button pressed then OK