I'm not aware of anything in Remote Buddy that would automatically do anything with your volume during launch or when selecting particular applications.

The only actions (and the only code) that change system volume are those provided by the "Audio & CD/DVD" Behaviour, and unless a button press leads to their execution or a volume slider in Remote Buddy's menu is used, I see nothing in Remote Buddy that would have an effect on system volume.

The Remote Buddy "Default Behaviour" has a mute action mapped to the "Select" button, though. Please check which Behaviour is active before you launch Plex (you can find the "Active Behaviour" by clicking on the Remote Buddy icon in the menu bar) and whether your remote sends that button code by any chance. In that event, Remote Buddy should also provide you with visual feedback about the volume being muted through that action.

Best regards, 
Felix Schwarz