Seems to me like `dbus-user-session` was the real culprit causing all the 
trouble.
I got it installed with anbox and that is when the problem started.

I got my keyring daemon to correctly start, the Login keyring to unlock
automatically while still being encrypted with my account password again
this way:

- Purge `dbus-user-session`, e.g. by running `sudo apt purge dbus-user-session`
- Revert files in `/etc/pam.d` back to their original state. I had commented 
out a line in `/etc/pam.d/lightdm` to work around the `gnome-keyring-daemon` 
not starting in the correct mode issue.
- Set my account password on the Login keyring again (using seahorse). I had 
removed the password and left the keyring unprotected to avoid being asked for 
the password each session.
- Set my user account password to something completely different and then back 
to my normal password using the `passwd` command. Before doing this, it seemed 
like the Login keyring and account password weren't yet synced correctly 
despite being equal. When I rebooted before the `passwd`, it still asked for 
the keyring password to be entered manually.
- Reboot. On my next login, it asked for the Login keyring password to be 
entered manually one last time, but offered a checkbox to enable unlocking that 
keyring automatically on boot, which I checked.

After this procedure, my system seems to be as good as new again.
Running 16.04 with vanilla Unity desktop and lightdm btw.

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https://bugs.launchpad.net/bugs/1689825

Title:
  gnome-keyring not unlocked on boot

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