Very mysterious dropping steps on one Y axis motor...I'm starting to lose it!!

[Hatchett Job]

Something I'm still not clear on, is I'm assuming you're relying on the settings in Mach to reverse the direction of one motor?

I'd suggest you set both axes identically in Mach3, then reverse the wiring to one coil on one motor, which will cause the motors to rotate in opposite directions.
This way both drives should receive identical step/dir signals, so any direction polarity issues will affect both drives equally.

This is exactly how I am currently running the machine but with both Y motors running from one output on the BOB.
If I give the motors separate outputs then Motor 'A' drops steps.