What I meant wasn't the status of the receivers itself but the indicator in front of the two "Apple Remote" entries.

Remote Buddy makes sure that for each remote type, only the signals of the best, highest resolution receiver that's attached to the system are used. That's why, when your system has a built-in Apple IR receiver, Remote Buddy will keep the Apple Remote for that receiver enabled and disable it for the EyeTV Receiver.

Now, what creates the issue at hand?

Since a recent change in Remote Buddy's EyeTV Receiver support code, the following happens: 
If a remote (whose signal comes in via the EyeTV Receiver) is deactivated, Remote Buddy takes care that all button presses for it are handled by EyeTV. 
This is problematic for the Apple Remote, because then an Apple Remote press can be handled by both Remote Buddy (received from the built-in Apple IR Receiver) and EyeTV (received via its own EyeTV Receiver).

The next release (of which I'll send you a beta shortly) will take this into account and make sure that, if you have another Apple Remote in your system, its signals won't be handled by EyeTV even if the remote has been disabled in Remote Buddy.

Best regards, 
Felix Schwarz