Yes--that is what the java folder should show.The coders wondered if there might have been a xerces.jar showing (as you have), which might explain your situation. Just move those xerces.jars elsewhere for now.
jum wrote a new build of LW that should address your problem. Go to
http://www.mager.org/LimeWire/LimeWire.html and download the 290 version.
He identified the error messages as relating to the file that keeps track of the incomplete downloads, called the downloads.dat file stored in the incomplete folder. If you install the jum290 version, all your current incomplete downloads won't show on the Search Pane, so you'll have to resume them from the Incomplete listing in the Library.
Did it work?