It's possible to disable the AUX input altogether. So yours could just be turned off.
I've done this on mine, because I never use it.
On the Stereo press PROG, then I think you have to press the far right button for the next screen and it should be there entitled AUX. You can toggle it on/off.

Did you try the above?
 
Strange.
Maybe they took the origional stereo out to replace a customers broken one?
 
It is an MY07, unfortunately the dealer I had dealt with is off sick so looks like I'll just have to wait until he is back
 
Well got to the dealer today, who then sent me to one of there other branches to see the guy that dealt with the sound systems and it turns out the radio doesnt actually have an aux function, the guy in the dealership is miffed. The aux input in the centre console is factory wired but he doesnt understand what is going on, so just have to wait until Seat technical department get back to them to see what the craic is.
 
My aux input hisses whenever I turn it on and it gets louder when I turn it up, is this normal or have I got a dry solder somewhere? just picked the car up on thursday :(
 
I get a lot of hiss as well - I guess the input gain should have been greater on the stereo. Altering the 'auxvol' as its labelled doesn't help either. Am beginning to wish I'd gone for the (albeit poor) iPod connector after all....