could it be somet to do with central locking? or key barrels? i had a strange prob like this last winter, and when i unlocked the car the windows went down and wouldnt go back up via the switches, did my nut in, but for some reason i tried getting in the car and locking via central locking, put key in ignition and windows went back up via switch, as should do, touch wood not happened again since,
not much use really, but if one of the lock mechs arent quite open/closed may sporatically trigger windows..?