It seems that there is a problem with the teeth of the belt not meshing well with the pulley. Every few rotations the belt rides up on a tooth and causes the movement to stutter. Hmm, to the forums I think.
[ Edit @ 21.03.11: After hooking up the motors and doing some testing it seems that this meshing problem doesn't cause the plate or head to jump. Perhaps the tension from the motor doesn't cause the problem whereas it does when moving by hand? Further tests to be done! ]