This doesn’t seem to have anything to do with the gnome-initial-setup
app.

It might also help to specify when, and how, you installed the apps.

** Package changed: gnome-initial-setup (Ubuntu) => flatpak (Ubuntu)

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https://bugs.launchpad.net/bugs/1788084

Title:
  Flatpack apps from software center not mounted after reboot

Status in flatpak package in Ubuntu:
  New

Bug description:
  Fresh ubuntu 18.04.1 install from USB image. Booted to live desktop
  and installed onto whole disk. After installation, rebooted into
  desktop. None of the three apps I installed (spotify, slack, discord)
  were visible in applications menu. Ran 'mount' from terminal, none
  were visible. After a subsequent reboot they were mounted correctly. I
  had already installed spotify from the .deb available on their site,
  so after rebooting my apps menu has two versions of spotify.

  ➜  ~ lsb_release -rd
  Description:  Ubuntu 18.04.1 LTS
  Release:      18.04

  ➜  ~ apt-cache policy spotify-client
  spotify-client:
    Installed: 1:1.0.80.480.g51b03ac3-13
    Candidate: 1:1.0.80.480.g51b03ac3-13
    Version table:
   *** 1:1.0.80.480.g51b03ac3-13 500
          500 http://repository.spotify.com stable/non-free amd64 Packages
          100 /var/lib/dpkg/status

  model name    : Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
  MemTotal:       16373892 kB

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