I have a 2000 neon and mine had the same problem, i would have to nudge it down the last inch when ever i thought it might rain and that , of course,
, didn't work well either and rain water would seep in...
so I took it in to the dealership ( warrenties are worth their weight in gold sometimes) and it was a fault in the track and was $450 to replace. Apparently all those black plastic quieter tracks get rough spots in them , they replaced it with a shiney metal one and i haven't had any problems with it since then, although it is a bit noise-y-er
(sidenote, i tried lubeing it before replacing it, as was advised by the family mechanic, didn't work
hahah)