In GNOME 3, the PackageKit update settings are now also put into "Applications", which means that searching for "update" in the overview brings up both "Software Updates" (the settings) and "Software Update" (the actual updater) side-by-side, which is very confusing.
Possible solutions to this problem are:
- Renaming "Software Updates" to "Software Update Settings" or something similar.
- Moving "Software Updates" into the GNOME System Settings (if possible).
- Remove "Software Updates" from "Applications" and make it accessible from the updater application itself only.
This was fixed in a recent version of gnome-packagekit.