Please make double sure you are running the latest version (by i.e. 
making a fresh download and replacing your current version with that 
download), because older versions of Plex do have the exact issue you 
describe. You can find more info on that in aforementioned thread, and 
an acknowledgment of the problem by the Plex team on their forum as 
well as user reports reporting the problem with an older releases of 
Plex and that all of them see it fixed with the latest release.

I'm sorry, but I don't understand your last sentence. If you mean that 
you set Remote Buddy to emulate Apple Remote presses and that these 
are not picked up by Plex, but are picked up by Front Row instead: 
This is another known problem of Plex, not of or with Remote Buddy. 
I've been in touch with the Plex team about it, looked into their 
sourcecode, looked through the source, identified the problem in their 
source and sent them both instructions how to fix it as well as a 
complete set of sample code on how to use the Apple Remote Receiver 
correctly. You should see these fixes in upcoming releases of Plex.

Best regards, 
Felix Schwarz