You never actually say if both windows go all the way down? If both windows go all the way down the top will work if the switchs in the doors tell the top controler "all is set"
I had a problem with mine and there is a switch in both doors that tell the controler the windows are down. If one of the windows doesn't go down all the way you're problem is probably in that door. If both go down fine my first guess would be to take the drivers door pannel off and jump the switch, the drivers gets more use.
It's a simple little two wire micro switch. I think it cost about $39.00