thanks for lengthy and detailed reply. 
As I have no known interference in my room, I believe that new alu apple remote might be the problem itself? If so, I have no way to resolve this issue right?

You also wrote, that FrontRow is not waiting for long presses and that it reacts immediately. Is it possible to configure remote buddy to act like this globally? That means disable the support for Hold (Long presses) and send keystrokes or codes to target app right after receiving it? Or remote buddy already does so and Plex needs to implement such a behavior?

I really appreciate your help - Thanks!