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Thanks for asking.
I have EyeTV and as such an EyeTV Receiver. Under the Remote Buddy menu this receiver is listed and underneath it it has an "Apple Remote". It appears this Apple Remote is the same as the main Apple Remote that appears under the Built-in IR Receiver listing. Then the EyeTV's "Apple Remote" is active every time I touch a button it gets processed twice—as if I pushed the button twice—once for the EyeTV Apple Remote, once for the Built-in IR Apple Remote.
Remote Buddy actually should automatically disable one of the Apple Remotes found on your system automatically because of the potential conflict you observe.
Which version of EyeTV are you running?
Is there a way to permanently disable this remote? Or even remove this Receiver completely (there appears to be no "minus sign" available in the preferences).
You can disable Remote Buddy / EyeTV integration regarding the remote control altogether by turning off support for AdHoc Receivers at Prefs > General > Advanced.
My "Apple Remote" is actually a Harmony One. I have no remotes paired with the Mac Mini in the Security control panel.
Are you using support for multiple Apple Remotes? Or are you using your Harmony One only as a six button Apple Remote?
Best regards,
Felix Schwarz