I think it's more that this is a very weird problem that no one has encountered before. Even if Limewire was using some port that Yahoo Messenger does, it should only be one port and from your explanation of the problem this involves several ports.

Only thing I can advise is maybe trying an older version of Limewire or even switching to a different client i.e. Frostwire or Phex to see if the problem persists.