[pfreivald]

If you can rule out programming and electrical, and can verify that your axles aren't bent, your chains are straight and of equal tension, etc, consider this:

Are both gearboxes greased? Were they both run a while to let everything seat well? We've found a noticable difference in performance between well-run and barely-run toughboxes, with well-run boxes being much smoother than their counterpart. (Just hook 'em to a battery and let 'em run for 20 minutes or so.)