[Toadling]

I use Control-` for my clipping shortcut and it has worked flawlessly ever since I installed OmniFocus last September. I haven't seen any problems at all. I'm on a recent MacBook Pro running Leopard.

This makes me wonder if there's some conflict with something else installed on your system. Have you tried creating a new user account and testing the clipping shortcut there? That would go a long way in eliminating some of the variables in this issue.