I also have had the same problem. I uploaded the java update for OS X, and still had the same problem.

The problem seems to be with the download manager that saves downloads still in progress. I had a file with the usual "requery" message sitting there. When I killed the download, I was able to quit Limewire without having it simply mimimize in the Dock. Which kinda makes that feature of Limewire useless <sigh>