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That's not it. I should have included more information in my post, to more precisely identify the problem, but I'll add it now:
I'm using OS X 10.6.2, Plex 1.16 with the latest firmware update, and Plex 0.8.5. No buttons are assigned to anything in Global Mapping. The six 'old' buttons are assigned to standard Plex functions in Plex (up/down/left/right/enter/menu) and the 7th is assigned to 'Context Menu.' Under this setup, in Plex, the Up button is not completely functional. Before I just said it didn't work, but here I'll be more specific: about 8 of every 10 button presses have no effect. Sometimes it will cause the cursor to move up in the menu, as intended... but it is rare and unpredictable. The other six buttons all work flawlessly.
The Up button does not have uniform functions - in various applications it does different things, from menu navigation to volume control to executing custom-written applescripts. All of those functions work flawlessly.
Changing the assignment of the button in Plex from Mapping->Plex->Navigation:up to Mapping->Virtual Remote->Virtual Button Press Up makes the button work flawlessly. The other six buttons are still assigned to their Mapping->Plex functions and continue to work flawlesly.
Frankly, this setup works well for me since I made that change, so I'm not too worried about the problem. But it is a problem, and I feel you should be aware of it. Based on my testing the remote control, the IR receiver and Global Mapping are *not* causing the problem. Based on my experience and reading a few posts around here, I see a pattern with three things popping up every time: 1) the new seven-button aluminum Apple remote; 2) Plex; and 3) the Plex functions in Remote Buddy's Mapping pane. The problem lies somewhere in the combination of those three things.