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More than likely the two windows that have problems have been replaced before. Someone broke one of my windows and the person that replaced it didn't line the window up properly and now my window does the same thing. It is annoying, but oh well. Hopefully there is some easy solution to turning off the pinch protection, but don't think there is due to safety issues.
Easy way is to roll up the window with the switch halfway. There are 2 positions on the switch. Momentary and full auto. On momentary mode I don't think it activates pinch protection.