I purchased with the same intentions and got the same results, I started with programming the Flirc with my Harmony setup as a MCE Keyboard and ran into conflicts within the first four directional keys. I skipped those and moved on the the numerical characters (1-9) and ran into a conflict after getting to the number "4". I looked at the Plex Player in the Harmony settings put it is limited to the amount of keys to program and then I would have to edit the keymap.xml file in XBMC which I was hoping to avoid by purchasing the flirc.
I was able to get my harmony working by using the IR learn command and programming the remote from my original Microsoft MCE Remote and then using that to teach flirc my settings. However, I still have an issue with having to press every key on the remote twice to get the flirc and xbmc to do anything. A bit cumbersome. Hopefully someone has a better answer, as I had great hope for this product.