ms,
There's an exploded view of a toploader here:
Exploded View of a Toploader
In looking at it, it does appear quite possible that the two gears could be misaligned enough to cause your problem. The drive gear's position is fixed - it appears - to the output shaft. If the tailshaft housing (item #65) was moved 1/16" toward the front of the car by omitting the gasket (item #69), the driven gear (not shown but is mounted inside the housing) would be misaligned with the drive gear (item #37) by the same amount.
There's also a very nice cutaway photo of the drive/driven gears here:
Cutaway View
It isn't obvious from the picture, though, whether a little misalignment would cause the gear to strip.
Maybe a picture of the stripped gear up close might help.
Just FYI,
Tom