I did some more fiddling last night and discovered that there is something going on during reboots that is messing up my flirc.
If I go to a windows PC and clear config, then reprogram I can plug it into my XBMC (openelec) and it will work fine, however after a reboot the GUI will automatically load in XBMC and after that everything goes down hill.
Is the GUI supposed to automatically load after every reboot? Any reason I can't just uninstall the GUI from my XBMC computer?