I setup my Harmony One for Plex Player and deleted all the virtual remote learning I had done with it. 
I configured Plex in Remote Buddy to use the virtual remote, according to the linked article, and I deleted the custom behavior I had built for it and deleted all the virtual remotes, and finally switched Remote Buddy to NOT use multiple remotes. 
I went into Plex and told it to use the Harmony remote, and I did NOT set it to be "always on".

As a test, I started EyeTV from Remote Buddy and its set to go into fullscreen mode. I then used Remote Buddy to start Plex. This seems to be working fine now. I have control over all the Plex stuff with the buttons on the Harmony beyond the few it uses out of the box. There are some timing glitches here and there and there is a definite lag, but this is much better than what I had before. This also disables directly launching Remote Buddy which I think is a good thing, but not sure. When I exit Plex, I come back to EyeTV which had been muted while Plex was running. That is all good.

So I decided to go into Boxee using the same approach. Without any configuration, it worked fine from Remote Buddy to go in and out of Boxee, but I wanted to set Boxee up to work like Plex. I went into Remote Buddy and mapped all the functions for the Boxee behavior to the virtual remote, just like I did with Plex. I then went into Boxee and told it to use the Universal Remote (Harmony) in the settings. I then tried launching this from Remote Buddy again. With these settings, I have nothing working in Boxee now. To recap, the Harmony is programmed for Plex Player and works fine with Plex. Boxee is set to use Harmony. Remote Buddy's behavior for Boxee is mapped to the virtual remote. Did I miss something in here, or shouldn't this work as I've set it up?