Everytime the battery is disconnected you need to re-initilaize the rear gate functions as well as the one-touch features like driver's side auto up/down and sunroof auto close/open. This is normal.
Discussed in detail here:
http://www.toyota-4runner.org/probl...window-roll-down-feature-stopped-working.html
The issue Martno996 is having is it seems the re-initialization needs to be done each time the vehicle is started. This is usually caused by a faulty battery. Have seen this many times with audio junkies running extreme systems, the battery just can't take it.
My question , which hasn't been answered, are all the one-touch features resetting (and the radio presets) as well or just the rear gate functions? This should help narrow down the possibilities