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In this case, Command-period is often used as a keyboard shortcut for the "Cancel" button in dialog boxes; depending on how each application handles keyboard events, they may not be passing them along to the services system for us to respond to, even if there isn't a dialog box open when you press it.

When you define the clipping shortcut in OmniFocus, does it appear next to the Send to OmniFocus menu item under the Services menu?

If the shortcut does appear there, it's set up correctly; basically, our services code has set up shop and is ready to accept events. Unfortunately, that doesn't guarantee we'll get them. We only get a chance to run that code on your selection if both the frontmost application and the services system in OS X send it along to us.

(I really need to update the sticky thread with a message that explains this; will do that tonight.)

In any case, if command-period is displaying in the menu item for the service, choosing another shortcut may work. For me, command-F6 gives a nice balance between "easy to trigger" and "unlikely to conflict with something else".

If the shortcut isn't showing up in the menu item at all, though, it's a different problem. If you contact the support ninjas, we'll be happy to help.