Ok, I been having the same thing with my car (and yeah sometimes launching into traffic circles worries me a bit). I just ran out to checked the air filter and it looks fine (still fresh after service). I am not sure how yours was mis-installed but it looks pretty idiot proof to me. There only seems one way to put it in (could be that my TT 1.8 2WD has a different configuration though - rectangular box).
I am no way a car fundi but I would have gone with a fuel system prob or transmission prob for this one too, not the air filter (see my post on dirty fuel line)
On the subject of air filters, if I can change the thread a bit, has anyone tried the K&N type filters in their TT. I have used them before and found them to be pretty good. I am considering installing one.