One thing I didn't mention is that at some point, my X axis started making a weird high pitch whining noise as soon as power was applied. I thought it was the bad wiring, but after the rewire it was still doing it. After swapping things around it seems which ever axis is plugged into the X stepper driver makes the noise. I woke up this morning with an idea of what is causing it and sure enough I was right. (Isn't it weird that you can go to bed with a problem and wake up with a solution?)

Anyway if you look at the schematic for my bob, detailed in this thread, you will see that parallel port 14 is used for X and A enable. I was using this pin for my charge pump output, so it was being pulsed at 12.5khz, which explains the noise. A quick pin swap has sorted that out but....

I assumed the purpose of the enable output was so that the motor didn't move without this signal being high. There was never a mention of setting pin 14 as an output in the original manual, so why does the X axis work without this set up in Mach3?