I recently had a very similar fault which may apply in your case also...
Customers driver's window dropped all the way to the bottom when opened and would not close.
The system works in this way:-
To open by inching, just the down signal operates.
To open automatically, the down operates followed by the up signal (down remains on).
To close by inching, the up operates.
To close automatically, the up operates followed by the down signal (up remains on).
By this method they can acheive the four operating states with just 2 signals, this may help understanding of the system and prevent control switches being replaced unecessarily.
In my case the up signal was invalid, being applied permanently. So when operated the window dropped completely. From memory the signals rest state is about 11V going to earth when operated.
Water ingress into the connector appears common and I found by disconnecting the control switch and checking the wiring for shorts that the culprit was the control module.
As the unit is so expensive I took the controller apart. You will need to remove the motor connector, I pulled the steel pin that feeds the hall sensor and screwed in a small self-tapper which can then be used to pull the connector out. The PCB then slides out. I desoldered the main connector and there was a tiny corrosion stain under it which I removed. I refitted the connector and put an acrylic PCB laquer on the board to keep the water out. I also filled the connector with silicon grease when I reassembled it. Sounds a lot of work but it was very straightforward, I would not have bothered but for the stupid price of a new unit.
Hope this is not too long but it may help others understanding of the system in the future.
Shaun.