OK, I've been trying to figure this out and I can't. I have a python script in ~/bin which does a bit of reformatting of text in the clipboard so I can paste it into a mail message. (Basically a fancy formatter)
I created a Unix shortcut in iKey so I could associate this with a key. The shortcut is as follows:
pbpaste | /Users/clarkgoble/bin/format_paragraph 2 55 "|" | pbcopy
Now in iKey this does nothing to the clipboard. But if I do this as a line in Terminal then it works fine, converting the clipboard.
Any ideas of what might be happening? I've tried putting full paths to pbpaste but to no avail.