After some more searching I have found Bug #54777 reporting identical behavior with some other applets as well. #54777 is yet uncomfirmed even though this is a very old bug, going back to Gnome 2.2 as far as I remember! I might actually get the source code and see if I can fix it myself.
** Tags added: autohide focus gnome-panel hide -- Auto-hidden panel fails to hide after losing focus https://launchpad.net/bugs/55260 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs
