My best guess here would be that the issue is your entire /var is on a
different partition that isn't necessarily ready by the time system
startup processes need it.
I'm going to add an upstart task for feedback from the upstart
maintainers if they would agree with that potentially being the root
cause.
** Also affects: upstart (Ubuntu)
Importance: Undecided
Status: New
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10.04: /etc/x11/xorg.conf deleted after reboot
https://bugs.launchpad.net/bugs/594613
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