My guess is that if everything else indicated by mrw was good, the problem is a microswitch in the latch. There are two in there. The plastic that holds them in place can come a little loose and stop the top from working. In mine, the one that lowers the windows, still usually worked, the other one didn't quite make contact.
Take the latch down, see if the plastic relay block is loose. Trigger the microswitches by hand. See if it makes a difference. Somewhere on the forum, I know there's comments about replacing that piece.