The fact the motors are still trying to move, tells us the drivers are still trying to move the motors, which leaves only two possibilities. Either there is something mechanical jamming, or there is some kind of glitch in the step pulse stream causing the motors to stall.

Where did you source the ballscrews?
Something like a bit swarf in the nut, can cause these kinds of symptoms. It just occasionally gets dragged between a ball and the screw, causing things to jam. Stop motion, swarf gets moved out the way, and things start running perfectly again. Only way to find out if this is the case, is to dismantle the nuts and clean them.

Noise could cause a glitch resulting in a sudden deceleration/acceleration, which could be enough to cause the motor to stall. However I'd still expect that amount of noise to cause other problems. Key things I'd be checking/double checking, is any shielding goes back to a star point, and you've not introduced any ground loops anywhere.