LimeWire get's the IP from java's InetAddress.getLocalAddress() function. That may or may not be the correct ip of your NAT and depends on how your system is configured.
If you force your IP you are always on the safe side. LimeWire will always advertise the forced IP of your NAT in the QueryHits, so people can connect to you directly after they received a QueryHit from you. Otherwise LimeWire might advertise your computers local IP address in your LAN in the QueryHits. The NAT does not know about Gnutella packages, it can only change low-level protocol messages like UDP/TCP/IP.
I wouldn't let LimeWire become an ultrapeer on MacOSX. The JVM is a little instable. Apple's implementation of Java 1.4 should fix this but the LimeWire version that is capable of using it is still in the works. (3.0 should be able to use Java 1.4).
The "file not found" problem is caused by corrupted HTTP requests. The old LW 2.8.6 was sometimes sending malformed http requests and old Gnutella clients don't request by urn, so LW will not always know which file to send, also resulting in a 404.
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