On 4 wheel drives you should keep all 4 tyres at a similar tread depth - on VWs it is around 3mm max difference - otherwise I think it can cause damage/wind up to the transmission.
As mentioned above, the quattro system tends to default to front wheel drive and adapts if necessary, so checking the tread on all 4 tyres is a good start. You might be inadvertently winding up your transmission.
It's something that I hadn't thought about because my VW was "always on" 4 wheel drive so it sounds like you need to rotate front and rear tyres for even wear with quattro drive.