Not sure if this is a bug in Scrivener or Lion: I’ve set three highlight colours to keyboard shortcuts, using cmd-alt-1, cmd-alt-2 and cmd-alt-3.
These won’t work at all until I go to Format > Highlight > Highlight text once after opening the program; then, magically, they start working. Any ideas?
I think this is more just a quirk of how custom keyboard shortcuts work in Mac OS in conjunction with dynamically generated menus. The Highlight menu is not a static thing, it can contain colours you save as favourites, and can show custom names if you change them in the Scrivener colour swatch palette. So the menu generates itself when you look at it, and prior to that point it doesn’t get custom shortcuts assigned to it. I had thought the situation was improved in Lion, but I just tested it out and you’re right, you have to visit that menu once at the beginning of the session.