1) Which versions of EyeTV and Plex are you using?

2) What do you mean with "Remote Buddy no longer sends commands correctly to Plex.". Please describe in this form: 
a) Actions you take 
b) The result you expect 
c) The result you actually get

3) The Apple Remote (as well as any button presses emulated by the Virtual Remote) is a global resource - and its input will - in the case of EyeTV and Plex - be received by the app that currently has focus / is the active one. Which app receives such events lies within the responsibility of the apps involved - Remote Buddy has no mechanism to influence this. So if your problem is about which app receives Virtual Remote events, I'm afraid there's nothing Remote Buddy can do about it.

You may, however, be able to get Plex to receive all input from the Apple Remote / Virtual Remote by setting Plex > Preferences >"Input Devices" > "Always Running" to "On".

Best regards, 
Felix Schwarz