Persistent "disk will be checked..." in the message of the day (motd) even after reboot

This is a known bug in Ubuntu 11.04 and apparently still exists in 12.04 LTS. What happens is what you described: you keep getting the notification even though there is nothing wrong with your hard drive and no checks are scheduled/will be done.

It's caused by the /usr/lib/update-notifier/update-motd-fsck-at-reboot script generating a /var/lib/update-notifier/fsck-at-reboot file with a timestamp in the future. The previous link has a convoluted solution from one of the Ubuntu maintainers (Steve Langasek), but it may be simplest to just do this:

  1. Open a terminal with Ctrl-Alt-T
  2. Type:

    sudo rm /var/lib/update-notifier/fsck-at-reboot
    
  3. Exit the terminal and reboot (or logout/login).

cat /dev/null > /var/lib/update-notifier/fsck-at-reboot

Fixed this for me....

Ubuntu 12.04.2 LTS.

3.2.0-51-generic #77-Ubuntu SMP Wed Jul 24 20:18:19 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

I had this same problem today - turned out in my /etc/fstab file, the line that had the relevant filesystem, had "0" in the last field, which means don't fsck it on boot. This should have been "1" for the root filesystem, or "2" for any other filesystem.

Also, my motd wasn't updated after the (successful) fsck. You can use this command:

tune2fs -l /dev/something

Then look for a line that says "Last Checked".