The problem has now disappeared after the last reboot. Before it, I did
this upgrade:

Start-Date: 2017-04-01  02:25:04
Commandline: apt-get dist-upgrade --yes
Requested-By: simple (1000)
Upgrade: python-samba:amd64 (2:4.3.11+dfsg-0ubuntu0.16.04.5, 
2:4.3.11+dfsg-0ubuntu0.16.04.6), libwbclient0:amd64 
(2:4.3.11+dfsg-0ubuntu0.16.04.5, 2:4.3.11+dfsg-0ubuntu0.16.04.6), makedev:amd64 
(2.3.1-93ubuntu1, 2.3.1-93ubuntu2~ubuntu16.04.1), samba:amd64 
(2:4.3.11+dfsg-0ubuntu0.16.04.5, 2:4.3.11+dfsg-0ubuntu0.16.04.6), 
samba-dsdb-modules:amd64 (2:4.3.11+dfsg-0ubuntu0.16.04.5, 
2:4.3.11+dfsg-0ubuntu0.16.04.6), samba-libs:amd64 
(2:4.3.11+dfsg-0ubuntu0.16.04.5, 2:4.3.11+dfsg-0ubuntu0.16.04.6), 
libpam-winbind:amd64 (2:4.3.11+dfsg-0ubuntu0.16.04.5, 
2:4.3.11+dfsg-0ubuntu0.16.04.6), winbind:amd64 (2:4.3.11+dfsg-0ubuntu0.16.04.5, 
2:4.3.11+dfsg-0ubuntu0.16.04.6), samba-common:amd64 
(2:4.3.11+dfsg-0ubuntu0.16.04.5, 2:4.3.11+dfsg-0ubuntu0.16.04.6), 
libnss-winbind:amd64 (2:4.3.11+dfsg-0ubuntu0.16.04.5, 
2:4.3.11+dfsg-0ubuntu0.16.04.6), samba-vfs-modules:amd64 
(2:4.3.11+dfsg-0ubuntu0.16.04.5, 2:4.3.11+dfsg-0ubuntu0.16.04.6), 
libsmbclient:amd64 (2:4.3.11+dfsg-0ubuntu0.16.04.5, 
2:4.3.11+dfsg-0ubuntu0.16.04.6), smbclient:amd64 
(2:4.3.11+dfsg-0ubuntu0.16.04.5, 2:4.3.11+dfsg-0ubuntu0.16.04.6), 
samba-common-bin:amd64 (2:4.3.11+dfsg-0ubuntu0.16.04.5, 
2:4.3.11+dfsg-0ubuntu0.16.04.6), wget:amd64 (1.17.1-1ubuntu1.1, 
1.17.1-1ubuntu1.2)
End-Date: 2017-04-01  02:25:28

But I can't spot anything related to the issue.

The message "*** /dev/sda1 will be checked for errors at next reboot
***" does not show up no more, and all the logs are ok:

root@serverlinux:~# cat /run/initramfs/fsck.log
Log of fsck -C -a -T -t ext4 /dev/sda1
Thu Apr  6 00:26:08 2017

/dev/sda1 has been mounted 31 times without being checked, check forced.
/dev/sda1: 646203/6725632 files (1.8% non-contiguous), 17524868/26880000 blocks

Thu Apr  6 00:26:16 2017
----------------


root@serverlinux:~# LANG=en_US dumpe2fs /dev/sda1 | grep -5 "Mount count"
dumpe2fs 1.42.13 (17-May-2015)
RAID stride:              32738
Flex block group size:    16
Filesystem created:       Thu Apr 15 15:23:07 2010
Last mount time:          Thu Apr  6 02:26:17 2017
Last write time:          Thu Apr  6 02:26:08 2017
Mount count:              1
Maximum mount count:      31
Last checked:             Thu Apr  6 02:26:08 2017
Check interval:           15552000 (6 months)
Next check after:         Tue Oct  3 02:26:08 2017
Lifetime writes:          5342 GB

"Mount count" and "Last checked" are now up to date (can't figure out
why).

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Touch seeded packages, which is subscribed to systemd in Ubuntu.
https://bugs.launchpad.net/bugs/1677305

Title:
  /dev/sda1 is checked at every boot instead of once every N mounts

Status in systemd package in Ubuntu:
  Confirmed

Bug description:
  Every time I login I get the message:

  *** /dev/sda1 will be checked for errors at next reboot ***

  /dev/sda1 is my root partition. fsck was successfully run, but it
  looks like systemd is not aware of this, so fsck will be run again at
  the next boot.

  root@serverlinux:~# lsb_release -rd
  Description:    Ubuntu 16.04.2 LTS
  Release:        16.04

  root@serverlinux:~# LANG=en_US apt-cache policy systemd
  systemd:
    Installed: 229-4ubuntu16
    Candidate: 229-4ubuntu16
    Version table:
   *** 229-4ubuntu16 500
          500 http://it.archive.ubuntu.com/ubuntu xenial-updates/main amd64 
Packages
          100 /var/lib/dpkg/status
       229-4ubuntu10 500
          500 http://security.ubuntu.com/ubuntu xenial-security/main amd64 
Packages
       229-4ubuntu4 500
          500 http://it.archive.ubuntu.com/ubuntu xenial/main amd64 Packages

  root@serverlinux:~# cat /run/initramfs/fsck.log
  Log of fsck -C -a -T -t ext4 /dev/sda1
  Wed Mar 29 00:26:26 2017

  /dev/sda1: clean, 612205/6725632 files, 17326020/26880000 blocks
  (check in 2 mounts)

  Wed Mar 29 00:26:26 2017
  ----------------

  root@serverlinux:~# LANG=en_US ls -l /run/initramfs/
  total 4
  -rw-r--r-- 1 root root   0 Mar 29 02:26 fsck-root
  -rw-r--r-- 1 root root 194 Mar 29 02:26 fsck.log

  [There's a discrepancy between the time in fsck.log and the time of
  the fsck.log but I suspect this is a UTC/CEST issue:

  root@serverlinux:~# LANG=en_US date
  Wed Mar 29 17:43:17 CEST 2017
  root@serverlinux:~# LANG=en_US date -u
  Wed Mar 29 15:43:21 UTC 2017

  The system was planned for reboot at Mar 29 2:25 CEST (Mar 29 0:25
  UTC)]

  This is the content of /etc/fstab:

  root@serverlinux:~#  cat /etc/fstab
  # <file system> <mount point>   <type>  <options>       <dump>  <pass>
  proc            /proc           proc    nodev,noexec,nosuid 0       0
  # / was on /dev/sda1 during installation
  UUID=c50edc7d-9f0b-4958-8e44-00bb5433ba42 /               ext4    
errors=remount-ro,noatime,nodiratime,commit=60 0       1
  # swap was on /dev/sda5 during installation
  UUID=93b413bc-8663-44b4-81de-1a225a2f90da none            swap    sw          
    0       0
  # /dev/sdb1 in ext4 250GB
  UUID=5f987a15-685a-4d2b-adf9-8bcde0eca04e       /data ext4 
errors=remount-ro,noatime,nodiratime,commit=60       0       1

  The output of dumpe2fs on /dev/sda1 is:
  root@serverlinux:~# LANG=en_US dumpe2fs /dev/sda1
  (...)
  Filesystem created:       Thu Apr 15 15:23:07 2010
  Last mount time:          Wed Mar 29 02:26:26 2017
  Last write time:          Wed Mar 29 02:26:26 2017
  Mount count:              30
  Maximum mount count:      31
  Last checked:             Tue Sep  6 02:46:17 2016
  Check interval:           15552000 (6 months)
  Next check after:         Sun Mar  5 01:46:17 2017
  (...)

  For some reason, "Last checked:" time is not up to date (see above for
  the content of /run/initramfs/fsck.log), hence the problem (I
  suppose).

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