Confirmed on an up-to-date dapper install. The dialog does seem to behave in a confusing way when these steps are taken.
** Changed in: gnome-panel (Ubuntu) Status: Unconfirmed => Confirmed -- Run dialog choses wrong application from known applications list https://launchpad.net/bugs/39711 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs