just as a sanity check,
why not try taking the step and dir signals going to the axis that works (x) and put them on one of the other axis drivers, for example y.
so since you know the x axis step and dir signals are good, when you move x in mach 3, physically the y axis of the machine should move instead. does it move?
do a similar test for z.
if teh axis DO move at least then you know for sure it is a problem with the signal between mach 3 and the step/dir output pins and NOT a problem with your motors or the connections from the stepper windings to your drivers/your drivers, etc.
i know you said the machine used to work, so it seems the wiring is ok but just double check since sometimes contacts corrode and conduct poorly etc... it doesn't hurt to check.