The major problem with using the other profiles (MCE/Plex etc) is the limit on the number of keys and the hassle of not having easy to understand 1:1 mapping.
In particular, if you use a Plex/MCE remote mimic in your Harmony, and you want to program the 'extra' harmony buttons at the top of the harmony remotes, which you can have an unlimited number of for doing all sorts of fancy things - you have to map each of these to some MCE remote button first and then program that in remote.xml to do what you want .... and pretty soon your run out of available remote buttons.
Far easier just to do a direct 1:1 mapping - set your Harmony up as a keyboard, then look at the list of keyboard commands in XBMC. Program each letter in the flirc software to be that button on the remote. Then you know your remote is sending 'P' for play, for example. And you can easily then use ALL keys, with modifiers etc....lots of buttons to play with.
I don't have (or want) any keyboard attached.
I will give the sensitivity settings a try and see if that helps. (My RC6 receivers already do just fine with the remote set to MCE remote mode so I don't really need the flirc to help me with that).
Jason - good support for this would make your product a lot more flexible again and I am happy to help with any testing etc required. Can flirc be started from the command line with some debugging output then?