[whpalmer4]

First, which version of Mac OS X are you using?

Second, can you confirm that the last click you made in the Mail window prior to invoking the clipping shortcut was on the pane listing all of the messages? If you click in the text of the message prior to invoking the clipping shortcut, you need to select something to clip (and that's just the standard clipping service, not the Clip-o-Tron).

On 10.6.8 with OmniFocus 1.10.4, I get the proper behavior when clipping single messages or threads.