I can confirm this is a Harmony\FLIRC issue.
I have a Harmony 900 and if I use the Default Panasonic or Samsung remote to configure Key mappings. I get fast key switching, or what appears to be multiple button pushes using these remote templates. I did not have this issue with my configuration until changing it to what was recommended here. So I reverted my Harmony configuration back to use the Plex device. Media Center PC\Plex\Plex Player. This device works without issue 100%. The only downside to this is it does use same signal codes as the Apple TV. So yes the recommended devices here may not conflict with other equipment; however they also cause this strange anomaly. Using the Plex Player as the default device from Harmony and configuring that per the XBMC keyboard commands works great. Sorry for the sloppy write up. Need to sleep....
My media center goes through:
1. Runco XP-OPAL65 for display
2. Pioneer Elite receiver HDMI
3. Homemade HTPC