I hate to pop your bubble but installing 2.5.5-Pro over the top of my existing 2.5.4-Pro had the following effects:
- lost all props
- blocked requests for file uploads until it had finished regenerating the hashes

I was starting to get worried that it might be ignoring the two sub-folders in my main shared folder, so I manually added them.

FYI - is there supposed to a be regkey the program checks? In regedit, I couldn't find anything like HKLM/sw/Limewire ...