I think it might have something to do with LW not being properly closed down when you shut your computer down. That's why I suggested to set it to close immediately (even though it may affect uploaders) so there's no instances of LW still running at comp. shut down time. LW being in the tray may keep some of the LW activities open. If you want it to sit in the tray when you use it that's fine. But for closing it down close it down completely. And open it from the Start menu. I only suggest this due to your particular problem.

Also it might be worth deleting your LW preferences folder whilst LW is closed (& must be fully closed.) Instructions are here: Fixes for Limewire