Ok, I've only been using Flirc for about 3 hours so far with my Harmony One.
After initial setup I also noticed that some of the buttons on the Harmony remote weren't doing anything, but instead of trying to map them in Flirc I instead added some mappings in 'Activities' (not the 'Devices') tab of the Harmony Remote software.
I edited the new activity I'd just set up (called XBMC) by clicking Customize Buttons. The top button (for example) is 'Menu' which I set using the dropdown to Device = Media Center PC and Command = ContextMenu.
I'm not running any beta software and I've not installed an add-on in XBMC.
What might be confusing the issue is that the Harmony remote uses it's own setup software that adds an extra bit of confusion to the whole thing. Fullscreen for example is a touchscreen button on my Harmony One and is not mapped to a specific hardware button.