[Chris is me]

Originally Posted by highlander

I'm not understanding something here then; if it wasn't bent, how could the gear possibly come out of alignment? Were the tolerances bad? Were your bearings messed up? Were the bearings really close together?

Not all deformation is plastic deformation. It's possible that with a cantilevered shaft, the forces of the gears interacting with each other, transmitted to the shaft, caused a small elastic deflection that isn't visible after load is removed (or barely visible under load even).

There was also 2 sprockets between the bearing and the gear, so possibly that was the problem.

This is almost certainly what the problem was and a detail you absolutely can't leave out. You have at least an inch of space between the bearing and the gear which is a much more dramatic cantilever than a gear butted right up against a bearing, plus the tension in the chain running on those sprockets could have contributed to elastic deflection. This setup has cantilevered gears that are much more well supported and thus less likely to lead ot issue.