Just a little update. I ran CCleaner and followed all the instructions! Then rebooted and re-installed Limewire (4.13) and started it up. It worked perfectly.

After an evening of usage, I shut my PC. The following day I restarted Limewire and got version 4.12 again (ooof).

Still no idea of whats going on and Limewire still appears all over my registry, even when its uninstalled.

Maybe I need a fresh approach! :P