Move the mouse cursor out of the way after closing a notification, and before looking for one.

Else, if the system is fast enough, the next notification immediately moves to
the exact place where the one we just closed was, and the mouse cursor (still at
the same place) highlights the cross button (even if we hide it with
hide_cursor), which prevents Sikuli from finding it and close the
next notification.
Press ESC before opening the GNOME run dialog.

In case the applications ("start") menu is open, ALT-F2 does not work.
Let's close the menu first.