I had basically the same problem last summer, only mine wouldn't go down. The problem on mine was the safety switches that are on the latches. After luricating and cycling the latches it worked slightly better but still had issues, so I just bypassed the safety. If I remember right there were two or three wires going to the switch on the drivers side and two of them had to be crimped together to complete the circuit, making the truck think that the gate was latched (thereby enabling the window to work). There may have been the same thing on the passengers side but I cannot remember if I had to crimp wires over there or not. Otherwise your problem could be a fuse or a relay (located about mid-bed underneath the interior panel on the drivers side). My geuss would be that since the electronics were exposed I all summer the problem in probably the safety switch. I hope this helps.
