From the FWIW department:
Besides the obvious: accelleration set too high, wrong pulse width, etc., I've had the steppers stall for three non-Mach related causes:
1) ways too tight . . i.e. el cheapo X2 with el crappo machinging has tight spots in the travel. Set the ways at the 'loose' point and it will jamb at the 'tight' point.
2) laptop/notebook with 'energy save feature' active. Slows down the CPU when battery gets low, or when it 'predicts' it is going to get low . . uh . . 'soon', . . . . or because it's Thursday, or for no reason at all. Causes instant stepper stall. Mine could be disabled in the bios and I removed the battery altogether and run off the charger. No more problems with it.
Some desktop processors also have forms of 'throttling' so look for that and disable it if possible. I would not swear to it as I am just now doing some homework on Intels 'Core' series architecture, but I think they have the ability to throttle. I don't know enough about that to be helpful, but it's worth a look in troubleshooting problems if these processors are used, methinks.
3) wrong (too high) resistor on a Gecko stepper driver. I hooked up a 4 amp motor to a Gecko 203V that still had the resistor on it for a 6 amp motor. The 4 amp would squeal and move in apoplectic spasms. Calculated and installed the correct resistor and it runs smooth as silk.