Krumz - You sir are a legend!
I thank you for your detailed instructions and I have now have a fully working roof after 4 weeks of misery. My local Audi stealer wanted £120 an hour to just look at it to tell me what was wrong. It's taken me a while to get sorted as I also had a broken bracket on the roof stowage box system but I've fixed that with "Q-Bond" (fantastic stuff) and now cleaned my pump and hey presto!
Just in time for the sunshine!
Abe - Mine was a Feb 07 (2006 car) and your symptoms sound exactly the same as mine! Check your roof box mechanism works properly first and nothing is broken then just do what Krumz says here.