Hello, I've worked a little bit on this in the same setup as Anarcat used, here at koumbit.
I've figured out why the users were not listed in gdm3. It was a line in /etc/pam.d/common-session that was missing: session optional pam_systemd.so with this line users are listed. This problem was caused by our puppetmaster crushing the file's contents, so it's not an issue with the upgrade process itself. I've also had issues with dependencies during dist-upgrade but I don't have good info to show here and I think the issues were with different packages. I'll try to get more info on this on the next upgrade. However I couldn't reproduce the initrd issue. The desktop rebooted in the new kernel as expected after both short and full upgrades. Maybe the difference was that I did not reboot between short and full upgrades and rebooted only once at the end of the whole process. Cheers
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