There are three common reasons for that happening.

1. You didn't set up the static IP correct

2. You forgot to save the router configuration.

3. Limewire changed the ports for some reason. Try going to Tools>Options>Advanced>Firewall Config and have a look if the port is still the same one that you chose.

BTW I don't know why a java icon would appear in the system tray. Sounds dodgy to me too. I have never seen it from running Limewire.