We got bitten by this bug and are now checking tables on our DBs.
What's interesting is that we made changes to the mysql upstart script
but they do not seem to be taking effect.  In particular:

1) changes to the kill timeout.  Changing the value to 300 had no
effect.  Even after issuing an "initctl reload-configuration", upstart
still appeared to kill mysqld after about 5 seconds.  We are still in
the process of confirming.

2) commented out respawn.  This also had no effect on "mysqladmin stop",
which would cleanly stop mysql, but almost immediatly, mysqld would
restart.  Here's a sample:

$ (  set -x ; sudo mysqladmin status ; sudo mysqladmin shutdown ; sleep 10 ; 
sudo mysqladmin status )
+ sudo mysqladmin status
Uptime: 92  Threads: 1  Questions: 7882  Slow queries: 1  Opens: 71 Flush 
tables: 1  Open tables: 64  Queries per second avg: 85.673
+ sudo mysqladmin shutdown
+ sleep 10
+ sudo mysqladmin status
Uptime: 11  Threads: 1  Questions: 919  Slow queries: 1  Opens: 49 Flush 
tables: 1  Open tables: 42  Queries per second avg: 83.545

This is on Ubuntu Lucid. 10.04 running mysql-server-5.1
(5.1.41-3ubuntu12.6)

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https://bugs.launchpad.net/bugs/620441

Title:
  MySQL upstart stop job does not cleanly shutdown mysql

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