Good to see I'm not the only one who's confused. Yes, I followed the directions.
Doesn't matter whether I plug the Flirc into my desktop or HTPC, it doesn't "react" to the Harmony at all. The Flirc software can see it (that's how it updated the firmware) but that's it. I can't reprogram buttons, or do anything at all with it, since it doesn't react to the Harmony.
Does it matter that I'm running XBMCbuntu?
You never answered my question about the setting for the Harmony. Do I need to have the Harmony set in a particular way? As I mentioned before, I added it as "Media Center PC 2" so that's what I had it set to when trying to control the Flirc, but it doesn't respond.
Is XBMC supposed to detect it as an input device? Because mine does not.