[Brian]

Tom - just for the purposes of experimentation, have you tried assigning a shortcut that doesn't involve a function key? You may have already tried this; just being thorough. :-)

Does something like option-control-6 work, for example?

On my machine, OmniFocus' preferences accepted a clipping shortcut of F12, even though that was already bound to the "Show Dashboard" item in System Preferences. It's behaving in a manner similar to what folks are describing - F12 shows up in the context menu. The entry shows up in correct spot in the shortcuts list in System Preferences, but there's no checkbox and pressing that button on the keyboard doesn't work.

So perhaps the problem is that there's a shortcut conflict - something else is already bound to the shortcuts that folks are trying?