It sounds like you may have binding in places. The slightest misalignment with your ballscrews and bearings can cause the motors to stall, which is what you are seeing.
I'd remove the motors, and turn the screws with your fingers to see if there are any tight spots. You need to check the entire length of travels.
What do you have the current and set to on the drives,and what are your microstep settings?
Does it stall at really slow speeds? Say, 50ipm?