Go into your LW options & this time, tick the box to run on system startup. Make sure to click ok or apply > ok (depending which version of LW you have). Close LW. Restart LW & go back into options & untick that box again > ok. Or apply > ok.
Sometimes, turning an option on & off can make it work properly.

If things are still stuffed then delete LW's preferences folder when LW's properly closed. See point 3 here & also point 2 if you've used older versions of LW in the past (there could be a folder in either location).
LimeWire Pref Folder in Vista
This will change all of your settings within options, you'll have to go back through afterwards & reset things. If you're not sure of your settings, go through LW's tools > options & write them all down, so that you can reset things later.