Thanks for the response. I can get the Apple Remote to work with Plex when Remote Buddy is quit by putting the "input mode" in plea to "Universal Remote". Unfortunately, if I launch remote buddy, it stops working.

Remote Control Diagnostics has the following errors while Plex is running:

PlexHelper (PID 1873) is using the Apple® Remote in exclusive mode 
While PlexHelper accesses your Apple® IR Receiver exclusively, no other application or OS X will receive Apple® Remote button press events. This can give you the impression that your Apple® Remote doesn't work. In that case, quit PlexHelper (located at /Applications/Plex.app/Contents/Resources/Plex/tools/osx/PlexHelper). 
Testing exclusive access 
Can't get exclusive access 
RCD's attempt to get temporary, exclusive access failed (error: The operation couldn’t be completed. (Mach error -536870203 - (iokit/common) exclusive access and device already open) (3)). This usually means that another application is already having exclusive access to the Apple® Remote. Neither OS X nor other applications will be able to respond to your Apple® Remote at the same time. This can give you the impression that your Apple® Remote doesn't work. Quit the application that exclusively accesses the Apple® Remote to make it available to OS X and other applications again.

What's the next step?

Thank you!