Windows: I had same issue, go to car menu -> setup -> remote key -> windows (or so) and check either or both front/rear and it will open and close with keyfob.
This is on your radio? If so, I am running an RCD550. Or is this on VCDS? I would think it would be in 46 Comfort> 10 Adaptation >channels 61, group 1 and 2 comfort open for 2 keyfobs and channel 62 groups 1 and 2 for comfort close.
MY May 2012 build has a BCM ending in H31 0333, not 0330 like kleinbus's earlier build.
Edit: Answer is on pages 53 and 54, specifically page 54 in the Owners Manual, at the very bottom, on how to activate this via your Infotainment Center, ie the Radio for us Old Farts and Luddites. I have included a how to video to provide the missing link from Kleinbus's original Post.
So, Kleinbus, did you ever get to play with raising your suspension? I really want to raise my T3 by 1-2 inches (not extreme) but haven't found anyone whose tried this. I've seen success with T1 an T2 models but nothing about T3 yet.