I think this is an OmniFocus problem. I can use clipboard history in a main OmniFocus window, but not in it's quick entry window. I notice that TextExpander doesn't work there either so OmniFocus must be doing something weird to get input.
It's not just Terminal.app.
I captured several url's and wanted to use clipboard history to paste them into a note field in OmniFocus. Bringing up clipboard history and selecting an entry took me back to the browser using that url.
I then tried to paste into Emacs and it worked fine. I went back to OmniFocus to try again but the url got pasted in Emacs. Pasting just doesn't go where I want it to go.
All apps are running on the main display. I have two other displays connected to this iMac.