Have you verified the signal names and the polarity? For instance, when I use my G202 stepper drivers driven by a PMDX-122 break-out-board, the X-direction is Parallel Port Pin 2, but if I use the G540, the X-direction signal is Parallel Port Pin 3. In other words, the Step and Direction signals are reversed.
Also, the G202 uses +5VDC as signal common, but the G203v and the G540 use 0V (ground) as signal common.
It seems like every time I change between the G202s and the G540, I have a moment of panic when I get the same type of problem that you're describing. As soon as I go into Mach 3 and change the port/pin setup, everything works as expected.