Hmmm, try installing it with out scanning you hard drive for files, it's one of the options during the setup. See if that helps.
If not try these suggestions. Try deleting the limewire preferences folder(while LW is closed) point 2 & 3.
Fixes for Limewire when LW isn't operating as it should!
Then try these again. Remove your current Java & then reinstall JRE using the offline installer here
http://java.sun.com/javase/downloads/index.jsp
Then reinstall LW using it's offline installer
http://java.sun.com/javase/downloads/index.jsp