Hello!
Same problem here. Ubuntu 16.04 LTS. Updated from 14.04 a few months ago. No 
problem back then but, since a few weeks, I had the same message. I haven't 
tried all these options but I just wanted to mention the fact that this bug 
still exists.

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You received this bug notification because you are a member of Ubuntu
Touch seeded packages, which is subscribed to upstart in Ubuntu.
https://bugs.launchpad.net/bugs/1504688

Title:
  fsck runs on every boot (clean install, single ext4 filesystem)

Status in upstart package in Ubuntu:
  Invalid

Bug description:
  fsck runs early on *every* boot (and always says "/dev/sda1: clean ...")
  The system was always shut down using the regular Unity mechanism (Gear->Shut 
Down...)

  Strangely, the "Last checked" time shown by "sudo dumpe2fs /dev/sda1"
  shows the date of installation and never changes.

  This system is a brand new, clean install from the 15.10 beta2 iso, with 
subsequent updates.
  I took all the installer defaults, which created a single ext4 file system.

  Please see attached:
    bootscreen.png - screen shot of fsck output at start of bootup (from VM 
window)
    dumpe2fs_out.txt - output from "sudo dumpe2fs /dev/sda1"

  ProblemType: Bug
  DistroRelease: Ubuntu 15.10
  Package: upstart 1.13.2-0ubuntu16
  ProcVersionSignature: Ubuntu 4.2.0-14.16-generic 4.2.2
  Uname: Linux 4.2.0-14-generic x86_64
  ApportVersion: 2.19.1-0ubuntu2
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Fri Oct  9 15:10:05 2015
  InstallationDate: Installed on 2015-10-07 (2 days ago)
  InstallationMedia: Ubuntu 15.10 "Wily Werewolf" - Alpha amd64 (20150924)
  ProcKernelCmdline: BOOT_IMAGE=/boot/vmlinuz-4.2.0-14-generic 
root=UUID=5944d29d-f058-4836-a160-4da2d77554e3 ro quiet splash
  SourcePackage: upstart
  UpgradeStatus: No upgrade log present (probably fresh install)
  UpstartBugCategory: System
  UpstartRunningSessionVersion: upstart 1.13.2
  UpstartRunningSystemJobs:
   Error: command ['initctl', '--system', 'list'] failed with exit code 1: 
initctl: Name "com.ubuntu.Upstart" does not exist
  UpstartRunningSystemVersion: Error: command ['initctl', '--system', 
'version'] failed with exit code 1: initctl: Name "com.ubuntu.Upstart" does not 
exist

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