This posting is older than 6 months and can contain outdated information.
Your problem for sure is not caused by Remote Buddy, which is actually very easy to show:
1) The Apple Remote OS X driver that Plex uses is a scarce resource: only one application can use it at a time.
2) When you get the default system response to a button press, it's a safe sign that no application is currently having a lock on the OS X driver and any application that wants to use it can actually use it.
3) Therefore, given your description, access to the Apple Remote is available to Plex, or any other application that wants to have it.
4) Why Plex does not try to use the Apple Remote on your system I can't tell. Remote Buddy for sure didn't change Plex' settings (there's no code in Remote Buddy that could even do this) and for sure doesn't keep Plex from accessing the Apple Remote on your system either.
5) Chances are you quit Plex' "PlexHelper" (which handles Apple Remote input for Plex), you turned off Apple Remote support in Plex, or PlexHelper doesn't try to gain access to the Apple Remote again when another application currently accessed it when PlexHelper initially launched.
6) Restarting "PlexHelper" and/or turning Apple Remote support in Plex on (or off and on again) may help. Please contact Plex Inc. for support on their product.
Best regards,
Felix Schwarz
