Quick check:

See if your options/preferences (depending on what platform/system you are running) are the same with both versions. Especially look at LimeWire's Advanced->Firewall-> UPnP (Universal Plug-and-Play) settings.

The newer versions improved the ability of LW to work with the routers that have UPnP built-in, but since you are using PPoE, that is probably the problem.

Perhaps you will have to use the manual settings.