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After all this time - still no answers !! Funny that I search the same issue and find my unanswered post !!
Please see the previous responses in the thread. Your question has already been answered fully in http://www.iospirit.com/support/forums/remotebuddy/singlethread/15363/ - before you even posted your question. Please read it.
The Harmony maps as 10 logical Apple remotes within RB.
1) Multiple remote support is designed and optimized for real Apple Remotes - not for use with Universal Remotes. The case where, on a six/seven button remote, you open a menu in order not to navigate that menu doesn't really occur for real Apple Remotes. At least I can't see that. If that'd be what you wanted with a real Apple Remote, you'd simply not open the EyeTV menu in the first place.
2) When you're outside of EyeTV's menu, you can customize the mapping of any and all multiple Apple Remotes and the actions will be performed accordingly.
I want to use the 'Exit' key within EyeTV menus to go backwards, ie. I set a keystroke on this button -ESC. Instead I get an 'up' command whenever I press Exit on the Harmony.
The up/down/left/right/menu/select buttons will navigate the EyeTV menu when its open ..
Chances are your Exit button on the Harmony Remote really sends an "Up" Apple Remote button code. And, as explained in the quoted text, when the EyeTV menu is OPEN, an "Up" button code will trigger what's logical for an Apple Remote: move up in the menu.
.. - and execute whatever action you've assigned to them when it's not open.
Applied to your scenario: your "ESC" key press is only issued when the EyeTV menu is CLOSED.
It's the side effect of using a feature for what it hasn't been designed for. That said, I'm well aware of the popularity of "abusing" this feature for Harmony Remote support - and am in contact with Logitech on this subject. And that's all I can say about this atm.