This is most likely a kernel issue.
The only thing Upstart does here is "down" the interface before issuing
the reboot call, could that be the culprit?
** Changed in: upstart
Status: New => Invalid
** Also affects: linux (Ubuntu)
Importance: Undecided
Status: New
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shutdown power off ethernet disabling WOL
https://bugs.launchpad.net/bugs/162201
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