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I'm able to set my copy of OmniFocus to use control-option-c as the clipping shortcut, so my suspicion is that something else on the machine is using that particular combination of keys.

Yep, if I try to assign a shortcut that another service is using to OmniFocus' clipping service, I get that behavior. You'll probably want to check the various other services in the Keyboard pane of System Preferences to see which one is using that shortcut.

(I'll also write up a feature request for a more informative message when this happens, if it's possible to add one.)