I re-installed the firmware and made sure to back-up my apps and the widget locations for the desktop (var/lib/gconf/apps/osso/hildon-desktop/applets).

When I restored everything, I first restored the apps and then I copied the (var/lib/gconf/apps/osso/hildon-desktop/applet) onto my N900 via SSH using WinSCP. After that I restarted the device but none of the widgets are showing up. I can only see the settings and remove buttons for each widget when I enter edit mode for the desktop as you can see in the picture below.