Answer Eddy's question first, but what your describing is resonance. When the machine is excited at particular frequencies, the vibrations will build up (like a tuning fork), so ideally you want to avoid these speeds or damp out the vibrations. One way to avoid them is to increase the micro-stepping resolution - this increases the frequency and can reduce the range of speeds at which resonance is a problem. One bonus of driving the ballscrews with timings belts is they have a noticeable damping effect.

If the motors aren't actually stalling you might be fine. A video may help...