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

Status in D-Bus:
  New
Status in chromium-browser package in Ubuntu:
  Invalid
Status in flatpak package in Ubuntu:
  Confirmed
Status in gdm package in Ubuntu:
  Confirmed
Status in gnome-keyring package in Ubuntu:
  Confirmed
Status in libgnome-keyring package in Ubuntu:
  Confirmed
Status in lightdm package in Ubuntu:
  Confirmed

Bug description:
  1) Release: 16.04.2
  2) gnome-keyring: 3.18.3-0ubuntu2
  3) Login. gnome-keyring unlocks "login" features including for google chrome
  4) gnome-keyring is not unlocked, chrome takes 2 minutes to open and with no 
secure password features(sync) functioning.

  For the past couple days, chrome on Ubuntu 16.04 takes a REALLY long
  time (maybe 2 minutes) to start. Once chrome is started, I am not able
  to sync and any secure password features are broken. I found out this
  is due to gnome-keyring not being unlocked at login. There's also no
  way to unlock the "login" portion of the keyring from the running
  daemon by default. I have to kill the gnome-keyring process and start
  without "--login" as a parameter. Then the "login" section shows up
  which I'm able to unlock. From there chrome starts up instantly but
  asks the following:

  Enter password to unlock your login keyring
  The login keyring did not get unlocked when you logged into your computer

  After that, all of it's sync and secure features are functional.

  Starting google-chrome-stable from a command line at boot without
  running the above workaround shows the following error messages:

  Gkr-Message: secret service operation failed: Did not receive a reply. 
Possible causes include: the remote application did not send a reply, the 
message bus security policy blocked the reply, the reply timeout expired, or 
the network connection was broken.
  Gkr-Message: secret service operation failed: Did not receive a reply. 
Possible causes include: the remote application did not send a reply, the 
message bus security policy blocked the reply, the reply timeout expired, or 
the network connection was broken.
  [4364:4393:0510/100407.740292:ERROR:token_service_table.cc(130)] Failed to 
decrypt token for service AccountId-108842767310111573264
  [4364:4445:0510/100407.740292:ERROR:gcm_store_impl.cc(929)] Failed to restore 
security token.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: gnome-keyring 3.18.3-0ubuntu2
  ProcVersionSignature: Ubuntu 4.8.0-52.55~16.04.1-generic 4.8.17
  Uname: Linux 4.8.0-52-generic x86_64
  ApportVersion: 2.20.1-0ubuntu2.5
  Architecture: amd64
  CurrentDesktop: GNOME-Flashback:Unity
  Date: Wed May 10 09:43:37 2017
  SourcePackage: gnome-keyring
  UpgradeStatus: No upgrade log present (probably fresh install)

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