I have a similar issues on a Bavaria 30 with an aftermarket installation. The windlass "shelf" is much shorter, too short to mount a horizontal windlass, so someone has installed a South Pacific vertical windlass, where the windlass body goes down through the back portion of the shelf and into the front cabin. I first noticed some dampness in the front cabin after heavy rain. The biggest leak is not the windlass seat, but where the back wall of the anchor locker/front cabin bulkhead butts against the ply shelf. They do not line up meaning lots of sealant has been used to fill the gap. Over time, water has worked down the gap, swelling the ply and leading to it rotting. I also have the same problem that the gypsy is too low, meaning the anchor chain enters the gypsy at an angle and it sometimes jumps off when weighing anchor. I'll need to cut out the rotten ply of the shelf and the back wall of the anchor locker, let in good stuff and glass it all up. It does seem that windlass installation is not always thought through properly on these boats.
