If its minor notches which go after a run then i wouldn't be concerned. As Ron says it will be minor inacuracies in the manufacture of the gears etc.
But, if its doing after some running it sounds like there is something wrong. Maybe a seized bearing? or the diff gear is shimmed too tight? (2 shims in the rear is the norm, i don't run any in the front)
how have you shimmed to shaft, could that be the problem?
Is it noisy on the track?
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