Hi Carl,
You got me stumped. Printed and read this post numerous times looking for a missing clue. What bugs me is the amount you are out and how it's varying. If the board elimination works you can forget these as I'm streching a little. I assume your motor is direct coupled to the screw.
MECHANICAL - Can you confirm that your motor to screw coupling is tight / not slipping?
SOFTWARE - Did you ever consider trying a later version of MACH?
Maybe somebody else can answer this question. Is there something in MACH like a home setting, etc
not apparent that could contribute to this? Maybe a dumb question but just thinking.
TUNING - Drop your velocity to say 10 IPM, adjust ramp for say 1/3 ramp up, 1/3 vel, 1/3 ramp down relative to time.
Don't use the Z axis during any of your x-y testing moves ( and just for kicks, set it just like the X & Y axis ).
Maybe you want to try upping the current setting on your drives up one amp.
PS: Didn't see anthing wrong with the file you posted, the quadrants are symetrical about the CL's, ran it. PLayed around with my mill and couldn't duplicate what's happening to you.
Just some thoughts and back to the sidelines.
RICH