This will happen if your comp crashes with LW open or if you shut down before LW's properly closed.
Downloads refuse to reload

What version of LW are you using? If you update to version 4.12.6, downloads should resume from wherever they left off in future...so maybe give that version a try
http://www.limewire.com/english/content/download.shtml
Sorry, but apart from that there's nothing I can suggest.