I have adjusted the RemoteMapping section to recognize the key from my lircd.conf. This has corrected my problem with almost all navigation issues with the exception of MythTV.
I have noticed that there are screen types recognized that do not seem to have RemoteMappings for:
10 12/03/05 17:40:35.352 Connect OK
10 12/03/05 17:40:35.415 Leeching
10 12/03/05 17:40:35.415 Requesthandler 0x806c828 (device: 38) ru
nThread now running
10 12/03/05 17:40:35.494 Screen type now M
M is not one of the screen listed.
I have been wondering if there is a way to have Pluto not send commands to MythTV and just use the lircrc file. It appears that the only commands that are sent twice are the ones that pluto also sends.
I have been playing around and the most function I have in mythtv is when I have the mythfrontend load the lircrc. I am going to experiement with commenting out the lines from the lircrc files that pluto also sends, but this seems like a very poor hack.
I will keep you posted if I am able to figure it out.