I don't know if this would fix the problem or not, but I did some looking around in there as I just had my door panel off because the clip that tracks along with the wire for raising/lowering the window broke.
Anyway, by the motor there is an adjusting bolt/nut arrangement.
The only other place that looked obvious to me for misalignment is the track that the rollers ride up/down in, maybe one of the rollers could be worn?
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