I had the same problem with water in the transmission; it turned out to be the shaft (SAILDRIVE) seal. It was replaced and end of problem, so far...
I later learned that this seal should be changed every 5 or 7 years and my boat is turning 7 this year.
By the way, how do you store/manage the transom "door"? I also have a 2003 Bavaria 44.
If you ever need to replace the seals on your portlights refer to my post / Replacing Seals and Lenses on Lewmar Portlights
You can write to me at firstname.lastname@example.org
, there are not many Bavs in this part of the world.