Found a bug, but just got hit by it again on another computer so I
think this might be more widespread and people won't figure it out
right away.
Gist is that if you have packagekit 1.1.4-2.fc25 (maybe on f24 also I
haven't tested that), when you click Restart & Install in
gnome-software, or check the Install Pending Updates in gnome-shell,
it won't actually apply the updates at next boot. You have to do 'sudo
dnf update PackageKit' reboot, and now the GUI initiated updates will
happen.
https://bugzilla.redhat.com/show_bug.cgi?id=1409268
--
Chris Murphy