I'm having the EXACT SAME PROBLEM, posted about yesterday but it's a few pages down. Chances seem good it's a problem with the wiring connector but I have not had a chance to dig into it yet. That seems to be the 2nd biggest cause of window problems.

Pacific Green '96 Contour LX V6 â??98 GTP, light mods, 14.66/94 Calypso Green '92 Mustang LX coupe, 13.56/101 Crown Autocross Club 1999 Street Tire Champion, 2000/2001/2002 Street Modified Champion KCR SCCA 2002 Solo II Street Modified Champion