I have just had similar problems to deeptank.
The battery was never disconnected either.
It all happened after my stereo install

started to think what have I done.
Thinking that something had locked up I disconnected the battery both pos and neg and tried again.
My problem had the drivers window operating only but not auto winding down and up. Finger control only.
None of the passenger windows would work either on the drivers control or on the individual switches.
The solution I found was to turn the ignition on whilst holding the drivers window control in the wind up position. After the key in switched to on, wind the window all the way down, then all the way to the top. The auto function will now work on that window!!!
Each window must have the same thing done at that window control, not the master unit on the drivers door.
Passenger rear door needs a long reach.
Once this is completed the drivers control will start working normally again and even with auto.
07 Prado GXL, D4D manual, silver and a fridge with constantly changing beer levels.