See this thread: http://ubuntuforums.org/showthread.php?t=1479423

This bug affects a number of people. Based on having been able to get it
working I have a guess as to what the problem is. First, here is what I
did to get it working.

Cron wasn't starting through upstart but it would start by hand. I went
through this process to correct it:

1) Boot/login
2) sudo service cron stop
   This would result in th warning message, "unknown instance,"  since cron 
wasn't running.
3) Reboot
   At this point upstart seemed to start cron, however, if I rebooted again, it 
wouldn't be running. So, prior to rebooting I ...
4) sudo service cron stop
  Again. This (I'm guessing) gave it a clean shutdown because it's been working 
ever since.

I'm guessing that, if state information about running services is kept
somewhere by upstart, that data can be corrupted. I also think the way
to corrupt it is to cut the power (or hard reboot) in the middle of the
boot process - though now that it's working I can't seem to get it back
into the failure mode - so this is a guess. I'm guessing this because I
repeatedly hard reset the machine while I was getting it set up (it's a
home theater PC running an unstable version of XBMC as the main
session).

Hope this helps.
Jim

-- 
upstart doesn't start cron automatically on boot in lucid for server on amd64
https://bugs.launchpad.net/bugs/592114
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