If you are running the clipboard manager, and then press Alt+F2 to run the command for which the text is on the clipboard, you can never actually do that. As soon as the runner pops up, the selection is replaced by the most recently run command. I suspect that this is because the gtk component incorrectly uses the x selection irrespective of whether it was a real selection, or an automatically chosen highlight. So the steps are: tell clipman to synchronise the selection and the cut/paste buffer highlight the word "xterm" in an xterm press alt+F2 press ctrl+V What is expected: "xterm" is the command to be run What actually happens: the selection is replaced with itself, and the cusor moves to the end of the selection.
If the program is putting something else in the primary clipboard, there is nothing the plugin can prevent. This is exactly what the GtkEntryCompletion is doing. It is making a copy of the current text selection inside the primary clipboard.
PS: a solution is of course a runner program that doesn't use the gtkentrycompletion widget. For example: gmrun gexec or even xfce4-appfinder which is more complete.