This posting is older than 6 months and can contain outdated information.
Hi Dave. I do run a HTPC with Plex. I currently don't have Plex added as a device to my Harmony because when I've tried this in the past I was never able to get RB and Plex to play nice. It seemed RB was blocking the remote codes from passing through to Plex so once I launched Plex, nothing would respond. (I was using the native Harmony support in Plex.) I then deleted Plex device from Harmony and have
Remote Buddy isn't blocking any codes. It interprets the codes and executes the actions that are assigned to the respective buttons just as specified at Prefs > Mapping > [Name of app]. If, instead, you want to pass through Apple Remote codes for a specific application, you can do this as well by selecting the respective "Virtual Remote action".
You can find details on this in particular (Harmony/Plex/Remote Buddy) here:
http://www.iospirit.com/blog/article/131/Remote-Buddy-and-Boxee-Plex-and-XBMC/
Best regards,
Felix Schwarz