PackageKit is the backend, the small background tool which does all the work. GNOME-PackageKit is the frontend, which just provides the UI. (Most stuff you reported is against the backend daemon "packagekit", not gpk so I reassigned it)
I already solved the issue you descibe above differently in Debian some time ago - it will flow back with the next Ubuntu release.
PackageKit is the backend, the small background tool which does all the work. GNOME-PackageKit is the frontend, which just provides the UI. (Most stuff you reported is against the backend daemon "packagekit", not gpk so I reassigned it)
I already solved the issue you descibe above differently in Debian some time ago - it will flow back with the next Ubuntu release.