Did absolutely everything...

Only setting this worked:

sudo vim /etc/systemd/system.conf

Let me tell you that this is an ugly mess.

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  limits.conf not applied

Status in jackd2 package in Ubuntu:
Status in lightdm package in Ubuntu:
Status in systemd package in Ubuntu:

Bug description:
  Since upgraded to 16.10 Yakkety, modifications in
  /etc/security/limits.conf are not taken into consideration when
  logging in the graphical interface.

  @audio   -  rtprio     99
  @audio   -  memlock    unlimited

  I tried the same settings in /etc/security/limits.d/audio.conf, to the
  same results.

  After logging in Unity, opening a console, the limits are not set:
  blablack@ideaon:~$ ulimit -l -r
  max locked memory       (kbytes, -l) 64
  real-time priority              (-r) 0

  Reloging to my user via bash DOES apply the limits:
  blablack@ideaon:~$ ulimit -l -r
  max locked memory       (kbytes, -l) 64
  real-time priority              (-r) 0
  blablack@ideaon:~$ su blablack
  blablack@ideaon:~$ ulimit -l -r
  max locked memory       (kbytes, -l) unlimited
  real-time priority              (-r) 95

  Switching to a console (ctrl+alt+f1) and logging in would apply the limits as 

  The exact same setup used to work fine on Xenial 16.04 before upgrade.

  If you need any more information, please let me know.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: lightdm 1.19.4-0ubuntu1
  ProcVersionSignature: Ubuntu 4.8.0-16.17-generic 4.8.0-rc7
  Uname: Linux 4.8.0-16-generic x86_64
  ApportVersion: 2.20.3-0ubuntu7
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Mon Sep 26 17:27:10 2016
  SourcePackage: lightdm
  UpgradeStatus: No upgrade log present (probably fresh install)

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