I have my Harmony 700 set up as a Samsung BR player (since I don't actually own no actual Samsung BR player), and the FLIRC emulating a keyboard... adjust the speed in the Harmony software, speeds seem fine to me.
http://forum.flirc.tv/index.php?/topic/22-harmony-remotes/
This post give some suggestions on which "virtual remote" to pick in your Harmony software to get the most buttons to map with XBMC.