There is a workaround for the Set-up That Won't Die problem. It worked for a misbehaving LimeWire Pro v2.7.3 on my G4 Mac running OS 9.2.2, and if you're missing a limewire.props file in your Preferences folder it might work for you.

But you need to have your previous LimeWire version's "limewire.props" file still available. I got mine from my last systemwide backup; it came from LimeWire Pro v2.6.5. Put a copy of the old limewire.props file inside the new ".limewire" folder located in the System Preferences folder. Make sure the copy has the original filename "limewire.props". After that you should be good to go. You can even change your preferences now and have them stick. Apparently all you need is one good existing limewire.props file in the .limewire folder to get over the hump.

Anyway, I hope this workaround also works for you. Good Luck.