When ticking the boxes and applying the changes it simply writes the new information to the appropriate settings file, which infact is most likely causing a conflict, hence not being able to connect.

If Limewire does finally connect and you see a change in the connection status at the bottom left of the application, it is important still, to untick the three boxes described, once they have been ticked. (If this makes sense.)

In other words, tick, "apply," now even if connection status changes untick and "apply."