The top position won't affect window operation.
The window relays are soldered to the immobilizer board, as I mentioned in the OP's other thread. If the windows drop when the top latch is pulled, the relays are fine. The problem most likely lies between the switches and the immobilizer.
I suspect bad connections or corrosion at the immobilizer connector, but no way to tell if the OP won't do the legwork, so I think I'll step away from this one.
