Try deleting your LW Preferences folder whilst LW is closed; instructions here: Point #2 & 3 in Fixes for Limewire (sample image included at bottom of page.)

Upon restarting LW you will need to reset all options. Now the two to be wary of are:
1. make sure Tools > Options > System Tray is set to Shutdown Immediately.
2. make sure Tools > Options > Advanced > System Startup is not checked.

Something else that can cause problems is having too many incomplete files, especially if some of them are really fakes files which drives LW crazy, so try Tip: Purge the Downloads Queue! (click on blue link)

Oh .. also make sure there is no limewire file in the system start up folder or settings.
And make sure your Java is up to date & properly installed. Online installations with java are risky & known to cause problems. Also having older version Java can cause issues with the newer java.

Limewire worked normal for a couple days, but the problem poped up again. Tried going back to the older version of java, deleting the hidden folder and incomplete files, but no luck so far. I've even reinstalled it just to make sure, going through all the steps again, making sure ALL files are gone before i reinstall limewire. But, when I am able to set-up my preferences again after deleting the hidden file, I'm not able to select some of the preferences. Example... I can browse and select which files to share, but not the check boxes below about sharing folders.
Anyways, it's weird. I'm not sure what's going on. Any other tips that might work??? I really like using Limewire!