I believe this is caused by the lack of a "Y/I/N/O/D/Z" prompt when the
package manager is trying to upgrade a config file which has been
"created by you or by a script". I had this happen when I first
installed Ubuntu Gnome 16.04 from scratch, I selected automatic login
and so the installer edited my /etc/gdm/custom.conf to reflect that. On
first boot, gnome-software showed I had updates,  but it hung
indefinitely after I told it to get them. I rebooted and reinstalled and
answered all the installer questions exactly the same, but this time on
first boot I did a dist-upgrade from the terminal (and avoided gnome-
software) and I got a Y/I/N/O/D/Z prompt for a /etc/gdm/custom.conf.

Steps to reproduce:
1. Install Ubuntu Gnome 16.04 or any Ubuntu variant which comes with gdm3 
3.18.3-0ubuntu1.
2. Enable automatic login (or hand edit /etc/gdm/custom.conf)
3. With gnome-software, attempt to accept software updates involving gdm3 
3.18.3-0ubuntu2

Gnome-software will just sit there.

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https://bugs.launchpad.net/bugs/1575351

Title:
  tell me I have OS updates and will not install said updates.

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