Refreshing PackageKit
It seems as this PkgKit has added a hook on pacman to run post-transaction, so it doesn't affect the operation of pacman, it just runs after every time pacman is used and produces this error. After what JM has forwarded I think it is best to remove it.
There is no promised support for anything gnome here (same shop with systemd pulseaudio, etc.) although plenty of gnome software, that are not bundled with the desktop, work quite well (gparted, gnumeric, abiword).