First off let me say gNet is a very cool world indeed. I am new to peer2peer, not new to Macs - I installed Limewire Pro (3.3.4) and after installing I got directory errors that only 3rd party software (DiskWarrior) could repair. Interesting I still have not seen mention of this on your website, this is not a known issue I guess ?
Mac Fixit seems to be aware of this... weird.
peace.

Apparently there is some sort of bug in Apple's java applications that Limewire uses that causes this. Limewire does not in any way, shape or form, change or modify system files.