I never had this happen to my 2nd gen yet, but I did have it happen to the 1st gen.
It was shortly after replacing the motor. I replaced the rivets with some rivets I had. They probably weren't as heavy duty as the ones I had to take out. They broke within a week.
I opened the door back up and put 1/4-20's in their place. No problem since.
Maybe you have some sloppy/broken rivets holding in the window mechanism?
Eric