When I powered the devkit from +5 and disconnected the USB cable, I couldn't get the FAULT LED to go away,

I tried powering the USB interface from +5 also, but that didn't work either.

I started checking logic levels with a volt meter, and found out that RESET* was always low even when I switches the DIP switch that's supposed to control it.

RESET* and ENABLE are transistor-or'd together so that either the USB chip or the DIP switch can control them.

Probing around told me that the transistor was not letting go of RESET* even when the USB interface was powered down.

So we cut the part out and now I can run the board just with STEP and DIRECTION inputs.