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can you just clarify what the difference is between following the pictures in the link you posted, and following your qualifying statement after (i.e. have the events sent straight to the system) - what does all this mean?
The instructions in the blog post only pass Apple Remote events through to the system when Plex is active.
If, however, instead you assign these actions under "Global mapping", they are always active - regardless of what application is currently active.
Remote Buddy uses its own event and driver infrastructure that's located on level above the OS X event system. When using actions from Remote Buddy's Virtual Remote, what happens is that Remote Buddy synthesizes events and passes them "down" to the OS X event system for the Apple Remote.
And can I just confirm - will doing this mean I can push "menu" on my apple remote and just have plex open as it currently does without remote buddy installed, and not have the remote buddy menu system open?
Given the information you provided and that you configure Remote Buddy correctly, that's how things should work afterwards.
Since I don't know your setup in detail, though, and the stock OS X Apple Remote driver provided by Apple has so many error sources that are completely unrelated to and outside of control of Remote Buddy, I can't give you any confirmation of anything, though. There are simply too many factors to consider - including, but not limited to other applications you have installed that may try to get exclusive access to the OS X Apple Remote driver at the same time Plex does.
You don't need to buy Remote Buddy in order to just try things out, though. We have a free, 30 day trial version available for download from the Remote Buddy website with which you can try out everything in your particular setup without spending any money.
Best regards,
Felix Schwarz