After upgrading from 11.10 to 12.04 Precise, I too suffered from the
unclean-shutdown->disk-check-on-every-startup problem.  I found the
cause of my problem last week thanks to info from the various posts
below.  I am reporting it here in case it is relevant.

At first, I guessed that Network Manager was to blame, especially since I am 
also having problems with a hang at shutdown which I suspect is to do with 
unmounting some CIFS shares.  NM however was not the cause but in following the 
advice in this bug report
https://bugs.launchpad.net/ubuntu/+source/network-manager/+bug/963106 
I added some diagnostic logging to the /etc/init.d/umountroot script as 
described in message #5.

This showed that plymouthd was still running at the time it should have 
terminated and this led me to this posting
http://ubuntuforums.org/showthread.php?t=2008576 
which in turn led me to
https://bugs.launchpad.net/ubuntu/+source/upstart/+bug/1019347 

I followed the suggestion in comment #7 of bug 1019347 and added the line
/bin/plymouth quit
to the /etc/init.d/umountroot script just before root is remounted read-only.  
(This is the same point that the diagnostic logging described in 963106 had 
been inserted.)

Result: clean shutdowns and no more disk checks on each and every start.

Now, it must be said that there are other candidates for the cause of this 
problem and it is worth looking at these too if you find that plymouthd is 
behaving itself on your system.  One that was relevant to me is ensuring you 
use the latest Nvidia driver if you use proprietary Nvidia graphics in your 
system.  Google for
12.04 nvidia shutdown
to find lots of reports.  I upgraded to the latest Nvidia driver but the 
unclean shutdown continued until I fixed the plymouthd problem.

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https://bugs.launchpad.net/bugs/998512

Title:
  Checking disk drives for errors at every boot

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