I've had this problem several times on different cars. I'm just acting questions here. Is it a "smokers" type window where the window kind of tilts as it goes up to allow a crack to stay toward the top front to allow smoke to excape, as on a mid thirties Ford truck. Also there should be two wheels or rollers that are in a groove below the glass. Is one of the 'popping out of the groove? Another problem I've had is one of the channels had broken or separated from it mounting point on the door. This will let the channel 'twist'. I would open up the door on the other window and try to figure out where the two are different. Good luck.

Six volt guy living in a twelve volt world