Ok, solved. My boot/shutdown sequences were wrong.

I reinstalled every package that owns a script under /etc/init.d.
Not a simple reinstall. Before each reinstall, I did a "update-rc.d -f <script> remove" because, correct me if I'm wrong, if rcN links already exist, installation won't correct them, unless specified in preinst/postinst scripts. Now, in util-linux.postinst, for hwclock.sh and hwclockfirst.sh, there's a "-f remove" before "start" and it's ok. Reinstalling initscripts and many other packages, doing this cleanup, sequence numbers have significantly changed.
Under /etc/rc6.d,
before         after
S01sendsigs    S20sendsigs
S01umountnfs.sh    S31umountnfs.sh
S01umountfs    S40umountfs
S01umountroot    S60umountroot
S01reboot    S90reboot
After fixing the scripts above, system booted fine. Then I fixed all the remaining. When is the last time the superblock is written? Isn't it when filesystem is umounted/mounted read-only on shutdown?
Could it be UTC time when it's umounted?

G.




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