Still troubleshooting...

The parallel port cable currently runs from the add on card (using 0xec00 address) to the breakout board. I've verified that the step pulses are making it to the drives by putting an LED light across the STEP (Term 11) and COMMON (Term 12) of the x axis and y axis gecko drives. The brightness of the lights vary with the step rate, at 10ipm the lights are dim, at 180ipm the lights are bright. I think the computer, emc2, parallel cable, and the BOB can be ruled out.

I did have a wiring error where I miswired the STEP/DIR COMMON (Term 12) on the gecko drives, I've now connected it to the BOB common terminal (I had wired it to the +5vdc external power supply, so I don't know how it worked before!).

I'm now double checking the wiring of the encoders.