When you set up the mapping for the Boxee Behaviour as for the Plex Behaviour, Boxee will get all Apple Remote codes as if Remote Buddy wasn't running or installed at all.

If, however, you already have Plex' Apple Remote support installed in "Always On" mode, please be aware that Boxee technically can't get any access to the OS X Apple Remote driver (even if the Plex UI is not running, because the "Always On" mode means that Plex's Helper application keeps an exclusive lock on it, which prevents other applications from accessing it at the same time. The solution here would be to not set any application's Apple Remote support to "Always On". Since you're using Remote Buddy to switch between apps, using any "Always On" option has no benefits anyway.

If you're running OS X 10.6.x, you can use Remote Control Diagnostics (=> http://www.iospirit.com/labs/remotecontroldiagnostics/ ) to find out whether, and if, which application is currently holding an exclusive lock on the OS X Apple Remote driver.

Best regards, 
Felix Schwarz