@ Axe:

You really have several users on a single machine doing LimeWire? I hadn't thought that this could be useful.
But yes, then every user should have his own configuration files. At least you need a dedicated port for every user to avoid conflicts. And I think the startscript (LimeWire) is looking for files in its own directory.
As for the program itself (LimeWireLinux.bin and the jre subdirectory) I would try to make a 'ln -s' to save space. I don't think you need to be owner or have write-access to that.