Today I was trying to use the 'clone' tool in Gimp and couldn't for the life of me get it to accept the source position with the normal 'control-click'. It seemed like it was being intercepted by something, as it turned into a little cross.
Turns out under Gnome you should go Applications -> Desktop Preferences -> Windows -> Movement Key and modify it to be something else other than the control key; then log out and back in.