From the RCD screenshot and description, it appears you're running several applications that try to access the Apple IR Receiver, namely:

- Prismatik 
- Plex (through its Plex Helper) 
- Remote Buddy

All three will seek exclusive access right after start as exclusive access is the only way of getting Apple IR events and making sure other applications - like iTunes - aren't launched and controlled by the system when you actually want to something else.

When you put your system to sleep, whatever application currently has exclusive access to the Apple IR Receiver will usually loose it. When the system wakes up again, the *first* application to ask for exclusive access to the Apple IR Receiver will get it. Who will get access is not predictable.

Basically, the path a button press travels right now is this: 
Hardware driver -> Apple IR system -> [three applications fighting for access, random winner after wake]

And I think that's what you're seeing here.

As far as Remote Buddy is concerned, it's in the (literally) unique position of being able to work around all the Apple IR randomness by offering its own driver. So, as a first step, please make sure you have Remote Buddy's driver (Candelair) installed. This ensures Remote Buddy will have priviledged access to the Apple IR receiver.

With Remote Buddy's driver installed, a button press travels this path: 
Hardware driver -> Remote Buddy -> [Remote Buddy mapping table] -> 
a) Behaviour handles event, nothing passed on to Apple IR system 
b) (Virtual Remote action only) passed on to Apple IR system -> [two applications (Plex, Prismatik) fighting for access, random winner after wake]

If you're using the action supplied by Remote Buddy's Plex Behaviour to control Plex, Remote Buddy will send UDP packets to Plex in order to control it. The path then looks like this: 
Hardware driver -> Remote Buddy -> [Remote Buddy mapping table] -> OS X local UDP networking -> Plex receives event and reacts

If you've, however, selected Virtual Remote actions at Remote Buddy Preferences > Mapping > Plex (or even .. > Mapping > Global mapping, which is usually the wrong place to do anything such), the path will look like this: 
Hardware driver -> Remote Buddy -> [Remote Buddy mapping table] -> Apple IR system (via Virtual Remote) -> (either Plex or Prismatik, whoever asked OS X first, random winner after wake)

In a nutshell: 
a) if you use several applications that all want access to the Apple IR receiver, make sure you have Remote Buddy's driver installed, or you'll get random results 
b) if you control Plex using the Plex actions provided by Remote Buddy in its default configuration, there's no additional step 
c) if you control Plex using Virtual Remote actions, make sure NO other application (other than the system's own "rcd", which is fine) tries to access the Apple IR receiver at the same time. You can easily check for the existence of any such applications using Remote Control Diagnostics.

Best regards, 
Felix Schwarz