A similar problem here...

I have my save & shared folder (same) on an external firewire HD. A few times I've forgotten to turn my external drive on before starting Limewire. I'm not 100% certain of neither my or Limewires actions in these cases , but Limewire forgets my default folders, nothing strange about that, maybe, if that were all to it...

What I don't like is, when I open up the preferences and selects my external HD (HD 80), Limewire now labels it HD 80 1. Next time HD 80 2. And then HD 80 3. If I manually change it back to just HD 80, Limewire doesn't complain. Now, I don't think I should have renamed it manually, bacause it seems like, as far as Limewire is concerned, HD 80 3 now is the proper name for HD 80.

When downloaded files just started to disappear from the surface of any HD, internal or external, I finally did some checking around. The files are impossible to find on any HD using a search program, BUT when using any open/save file dialog box, behold, there's a couple of folders (shared, shared, HD 80 2, HD 80 3, and so on) in the scroll menu (places, locations, whatever, I don't have an English OS) which I can actually browse! With the right program, I can at least open them...

Maybe you have to logon OS X as superuser to salvage those files, as they seem to be stored someplace... well, else. Half out of reach for my admin account. I'd be happier if Limewire could save files to a temporary folder I actually have access to when the original folder is unavailable, instead of doing whatever it does...