Ah--the file is supposed to be recreated to give you a fresh start. The startup file is the gnutella.net file, which lists the addresses that allow you to connect to gnutella the first time. After that, addresses come from other connected hosts.
If the Free won't connect, Pro won't help either, but you should be using th latest Free version (4.0.4 downloaded from limewire.com)
You can try the quick test
http://www3.limewire.com:6346/ and see if there's a block somewhere (the page *should* say "Your test page was a success!")
If not, you'll have to plod through all the steps of figuring out where your communications to the gnutella network are being stopped. (Firewalls, Routers, ISP's ).
Sorry--but best wishes anyway.