I installed your last release and I observe status-menu.plugins file. I attached to you the original and the file after installation of advanced clock plugin. As you can see your installation delete some parts of my file:

[profilesx-sp-plugin.desktop]
X-Desktop-File=/usr/share/applications/hildon-status-menu/profilesx-sp-plugin.desktop
X-Status-Area-Position=18
X-Status-Menu-Position=20

[wifi-switcher.desktop]
X-Desktop-File=/usr/share/applications/hildon-status-menu/wifi-switcher.desktop
X-Status-Area-Position=18
X-Status-Menu-Position=21

[simple-brightness-applet.desktop]
X-Desktop-File=/usr/share/applications/hildon-status-menu/simple-brightness-applet.desktop
X-Status-Area-Position=18
X-Status-Menu-Position=22

[quick-launch-sb.desktop]
X-Desktop-File=/usr/share/applications/hildon-status-menu/quick-launch-sb.desktop
X-Status-Area-Position=18
X-Status-Menu-Position=23

could you solve this?