I had a similar problem. Not being aware of the forum, I sent a help call to Limewire and received a very helpful reply suggesting that I uninstalled both Limewire and java, replacing the java from:
Archive: Download Java 2 Platform Standard Edition (J2SE) 5.0 Update 10
and downloading the JRE version using WIndows offline installation.
On reloading Limewire Pro, everything was fine.
It would seem that it is the LATER version of java which has the problem, as this suggested download was an archived version.
I also noted that Limewire only vanished when the screen saver kicked in. If that was disabled, there were no problems.

The only thing now, is that from time to time, one of those annoying bubbles pops up telling me that there is a java update available.....