I finally got my JGRO put together and running after several years of staring at my controller board from HobbyCNC (4aupc rev2).

Specs:
JGRO standard build, nothing fancy
3/8 all thread drive screws (doing this on the cheap for now)
Cutting board backlash "nuts"
36V 9A power supply
425oz Hybrid Steppers
LinuxCNC (formerly known as EMC^2) v 2.5.2

So far things seem to work "ok" except for the fact that two of the axis are moving at what appears to be roughly half speed in the positive direction.

X-axis, moves fine in the (-) dir, but half speed in the (+)
Y-axis, moves fine in both dirs
Z-axis, moves fine in the (-) dir, but half speed in the (+)

I have the board set to 1/2 step (it was 1/8 with same problem).

Any idea what I might have messed up?