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Woohoo! It's working perfectly now!
I agree that it would be cool if Remote Buddy could specifically support the Harmony as a single remote, but I can understand Felix's concerns about trying to support something that he didn't start. I'd hope the Plex developers would give him the names of anyone that's been helpful at Logitech. For that matter, I'd much rather the Plex guys work on improving the media experience, not on supporting remote controls!
One request I have is a confirmation dialog for the "Rest to defaults" button in the mapping preference. One accidental mouse click there will ruin your day if you've got a custom map on ten virtual remotes.