Hi, Fred
Reg: "When I use the MPG the “Y” axis is backwards from what I think it should be".
In your Ports and Pins, Motor Outputs, Are all your Axises set to the same Dir LowActive, ether X or Checked ? (thy should all be the same)
In Motor Home/Soft Limits, Reversed Box should be used to change Axis Direction?
If this doesn't fix it, You need to swap your stepper motor wires on the rev axis to solve this, (4 wire stepper, Swap A & A-), ( 5-6 wire stepper, Swap 1234
to 4321), Then un-check the Rev. Box.
I've sent you a PM (top of this page, User Info) or PM your Phone #.
Hope this Helps, Chip