I have almost the exact same problem:

-LimeWire doesn't completely shut down and still remains in Task Manager.

-Replacing the gnutella.net file did not help.

-Changing the port LimeWire uses froze LimeWire.

-LimeWire used to work with ZoneAlarm but this new version screwed up everything.

Meanwhile, I have decided to try using FrostWire, which is an alternative to LimeWire.