I am surprised there isn't a newer harmony linux thread... Last post here is over a year ago...
I have my harmony set up with the two devices, XBMC (sw) and Media Center SE as described here:
http://forum.xbmc.org/showthread.php?tid=95063 (yeah, it's for Windose, but it should still work, right?) The keys and extra buttons that I have defined with Media Center SE and half of the XBMC (sw) don't seem to be sending anything out that my computer recognizes. I ran irw, and when I press those buttons, nothing happens (it works fine for the . But I do know it is transmitting SOMETHING because I have a USB-UIRT hooked up to a different computer and I can see the activity light come on when I press buttons on the remote. So, where do I get started? My lircd.conf file includes /usr/share/lirc/remotes/mceusb, and I have not made any changes to it.