If these are wired in a unipolar manner - which is sounds as though they are... you will need to isolate the centre taps. I appreciate the buggeration that comes with this - and recognise that at this time you're probably trying to keep the machine in a recoverable format (normally I'd just cut/isolate the cable at the stepper), but I understand you may want to be a bit more circumspect. the centre tap will be either to ground or to +V and it'll be causing problems for the driver - certainly your described behaviour I can imagine with the centre taps connected.