You lft out one crucial detail:
When the system creeps, do the DROs in mach show any change? This is fundamental.
Change: something is telling Mach to creep along. I suspect this is not happening.
No Change: Mach is not putting out any Step pulses, but the hardware thinks it sees some. And it only sees the puses when the Dir line is in one state, not in the other state.
I would check the power supply to the controller - both the +5 V rail AND the 0 V rail. You want hard single-point (star) earthing. It sounds as though one of these lines, and i suspect the 0 V, is wobbling around.
Cheers
Roger