I started running into similar problems as once before ( http://mysettopbox.tv/phpBB2/viewtopic.php?t=5382 ) and ironically, I can't remember what fixed it last time, I think it just kinda worked itself out after I played with it enough. As a side note, I'm actually doing all this troubleshooting remotely over the phone with my dad. (yeah, I know, I should setup ssh or something)

Anyways, I started running through some of the things I did then and I started off with redoing mythtv-setup. I killed the backend and cleared the settings but when I went to put in the channel lineup stuff and hit finish, it didn't save. I tried several times and with reboots inbetween and nothing changed. I'm really not sure what would cause this.

I'm tempted to just say upgrade since its now a couple versions back but my dad is wary of doing it while I'm not home and I'm not convinced that it will keep all the data with the database being in a weird state. Any ideas or is it time to try R5D1?