Do a safe boot & repair permissions. That's a start. And remember a safe boot will take a lot longer to start up as you found out last time. In Tiger during the safe start it eventually comes up with a window asking if you want to continue with a safe start, press yes or continue. Of repairing permissions reboot normally.

If this doesn't help, then delete your LW preferences found here: /Users/your_username/Library/Preferences/LimeWire

If reinstalling Java didn't help, perhaps reinstalling Tiger might help using the latest offline updater that includes all previous updates. That's a big download though.