What pitch are the ballscrews, and what are your velocity and acceleration settings?
When slaving, both axis must use exactly the same settings. I would guess that the calibrate function either won't work correctly, or you'll need to copy the settings to the slaved axis.
If the two axis are not moving in sync, then most likely, one (or both) motors are losing position. This can happen for a variety of reasons.
Generally, 425oz motors don't perform very well unless you run them at 70V or more, due to their high inductance. They can easily lose position if you're trying to spin them fast.
Also, it's very common with modern PC's for the G540 to require a very high pulse width. This is due to the PC having a weak parallel port. Try setting the pulse width in the motor tuning screens to 15.