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Thanks for asking.
The Harmony Remote is not currently supported by Remote Buddy.
What the Plex profile is doing is send the Apple Remote IR codes of several different Apple Remotes and distribute them over the buttons of the Harmony Remote. However, that profile is really only usable with Plex and is not suitable for general purpose use: it contains too many errors in IR code programming (leading to long presses not working - or a long press sending the codes for lots of short button presses), the use of IR codes often isn't consistent with their meaning (you already mentioned an Apple Remote "down" code being sent for "Exit") and the profile even lacks codes for some buttons of Harmony Remote.
This topic has come up and answered by me many times before in this forum, so if you're interested in technical details, please take a look at past topics.
However, how do I get the other keys of the Logitech Harmony 700 remote mapped or passed through as they normally are without RB running?
Follow the instructions at
http://www.iospirit.com/blog/article/131/Remote-Buddy-and-Boxee-Plex-and-XBMC/
to simple pass through all Apple Remote button presses to Plex - which can then react to the button presses directly. There's no necessity at all to perform any complex and time-consming setup as described in the piece you linked to in your follow-up post.
I recommend to use the Plex profile only for Plex (in combination with the simple pass-through configuration described in the IOSPIRIT Blog) - and the regular "Apple Remote" profile (which sends correct IR codes for short and long button presses) for everything else.
Best regards,
Felix Schwarz
