My makerbot thing-o-matic has a problem with a drifting y axis, but only when a layer is complete. There’s lots of vague advice about how tight or loose the timing belt should be, but I’ve tried a dozen different tension guesses, and nothing seems to work without shifting the print mid-way through.
edit 2012-02-01 : my voltages were set to the makerbot motors, where the should have been set to the moons motor voltages. :-