I did some searching and this is what I found, I don't know if it will work but I'll try...
This is how to rerest the windows. This is how it's done at the factory.
1 - While the window is in motion, either up or down, disconnect the battery or pull the fuse. I think it is easier to diconnect the battery. It is important that the window is in motion while losing power.
2 - Wait 1 minute and reconnect the battery cable. After the cable is secured to battery post, push or pull both window buttons so that the windows go all the way up and then all the way down. You will hear a little click (usually) when it is almost to the top. This will relearn the window module. Done.
Hey, I don't know if I'm too late for this, but better late than never right?
I had my windows tinted on my 06 v6 a year or two ago and came across this problem...
My window tint guy simply opened my door and on the actual door, left side; middle (where the lock catches the small metal bar on the door frame; sorry if I'm explaining this bad) there's a insert-like mechanism that can go up and down. After messing with it a couple times he was able to get the window back to regular operating order.
Again, sorry for the terrible explanation. I'll try to include a picture!