Good luck! if that's what it is, you can remove the battery, then the battery tray, and use a screwdriver or something to get the debris out of the drain. Some say removing the rubber piece in the drain helps this from happening again.

 

The same thing actually just happened in my B6, I'm just wondering if you found out what was causing this. First thing that came to my mind was my air vents too, was that the problem?

 

Yup..happened to me a few months ago after a huge rainstorm. My TCU had water damage, as well. Epic suck.

 

It's was coming in through the hole in the firewall where the ECU wire bundle goes through. The water "runoffs" in the battery/brake/ECU compartment were clogged with leaves, water fills up and leaks in through the wiring and down coming out from behind the clutch foot rest. I also recently received a piece of mail that explained to me that I ( and you, being an A4 owner within the model year specified ) am entitled to reimbursement from VAG of any money paid out to a licensed shop for repairs to damaged interior/exterior components caused by water accumulating and seepage. This also includes the brake booster, b/c of how low it sits in the compartment, it is common for water to breach the booster causing a loss of vacuum pressure and poor brake response.
Here is the website with info on the class action suit against VAG for this, whether or not you (and your car) qualify, and pdf application for reimbursement.
wateringresssettlement.com
Good Luck!

 

thanks a lot, ill have to check out that webpage!