Running Mavericks, installed clip-o-tron 1.0.1 and I assigned it a shortcut (cmd-opt-,) in Keyboard Prefs.
When I highlight a message in Mail and hit the shortcut, it just beeps. If I selected OmniFocus: Send to Inbox from the Services menu, it works as expected. I even see the keyboard shortcut there in the services menu.
Keyboard prefs shows no conflicting keyboard shortcuts, either.
I’ve also suffered this for a while. Both in Yosemite and El Cap
Update, and fix for Clipping Mail messages:
keyboard shortcut to ‘Omnifocus 2: Send to Inbox’ Text Service
WORKS BUT you have to have Text Selected.
Based of How do I clip email items to the Inbox in v2?
My workflow is no longer to select the message in the left pane, but to select some text from message itself. Say a key sentence, the title, or the whole lot