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Thanks for asking.
Remote Buddy can only react to what it receives. It doesn't know the layout of customized virtual remote and can't take it into account.
So, if you're using a Harmony profile where the Menu button doesn't send the Apple Remote menu code, that's most certainly it.
If your Harmony sends an Apple Remote Menu button press, this will hide the Remote Buddy menu without any further navigation.
Best regards,
Felix Schwarz