I had my own share of headaches trying to get my Aura to work after my Leon almost ran out of battery (I took it out to recharge it). In my specific case, the code attached to the manual was not working (lost about 4 hours between attempts -- so frustrating).
I started to suspect that the previous owner had most likely replaced the unit (probably under warranty) so I decided to take the whole thing out just to confirm the serial number would match to the info I have on the manual before spending money on a new one.
Result: The previous owner had indeed replaced it, as the serials didn't match, and this is why it wasn't accepting the code I had there.
Luckily, they had written the code of the new stereo directly on the unit itself and I got it working.
Just wanted to post this in case someone else is facing the same issue, as I have seen quite a few people on some forums (not here) suggesting that "if the code isn't being accepted and it's correct, the unit may be faulty".
Before shelling out money for an aftermarket system (and transforming your CD changer into an ant farm or similar), take your unit out and check your serial number.
Taking the unit out is VERY easy. Get a pair of scissors or a narrow knife (it must go through the horizontal holes and get to the small plastic clip that lock it in place) -- just give it a little push until you hear it clicking, then move on to the next (I did not need to push both of them at the same time, so I assume you won't need that neither).
Once both have clicked, just wiggle it a little bit and pull the unit out (I just pulled it from the cassette deck as that was the only thing I could pull it from without scratching it from the sides or anything like that --- didn't wanna do that).
The serial number will be engraved on the right side of the unit, and a label with the same number will be on the top or on the right side as well.
With a bit of luck, it's possible that the previous owner or electrician wrote the code either in the label or somewhere else on the unit (it's common, as it saves headaches and that won't really prevent someone from breaking into your car anyway).
Good luck!