In our network, we currently run 6 versions of java. I just wrote an installer that is being used to correct all of our java issues since we can't use one of our web apps due to some weirdness. Anyway, if you want to try to correct the java, if that is what's wrong, do the following.
Uninstall all installed java. Then Delete the HKLM\software\Javasoft registry key. Open you profile dirctory, i.e. C:\documents and settings\user1 and delete the .java directory. Also, Delete the C:\program files\java directory and all other java dirs that might exist there.
Then reboot. Install the progam you need for limewire, (I don't know, don't use it...) ansd see what heppenes. This is the basic process that we use, and it's working for use. Just so you know, java is order dependant. basically, you have to install them all in order as an older version will make changes to the newer setups causing issues.