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I am running Debian 7 stable with unattended-upgrades (every morning at 6 AM) to make sure I am always fully updated. I have the following config:

$ cat /etc/apt/apt.conf.d/50unattended-upgrades 
// Automatically upgrade packages from these origin patterns
Unattended-Upgrade::Origins-Pattern {
        // Archive or Suite based matching:
        // Note that this will silently match a different release after
        // migration to the specified archive (e.g. testing becomes the
        // new stable).
//      "o=Debian,a=proposed-updates";

// List of packages to not update
Unattended-Upgrade::Package-Blacklist {
//  "vim";
//  "libc6";
//  "libc6-dev";
//  "libc6-i686";

// This option allows you to control if on a unclean dpkg exit
// unattended-upgrades will automatically run 
//   dpkg --force-confold --configure -a
// The default is true, to ensure updates keep getting installed
//Unattended-Upgrade::AutoFixInterruptedDpkg "false";

// Split the upgrade into the smallest possible chunks so that
// they can be interrupted with SIGUSR1. This makes the upgrade
// a bit slower but it has the benefit that shutdown while a upgrade
// is running is possible (with a small delay)
//Unattended-Upgrade::MinimalSteps "true";

// Install all unattended-upgrades when the machine is shuting down
// instead of doing it in the background while the machine is running
// This will (obviously) make shutdown slower
//Unattended-Upgrade::InstallOnShutdown "true";

// Send email to this address for problems or packages upgrades
// If empty or unset then no email is sent, make sure that you
// have a working mail setup on your system. A package that provides
// 'mailx' must be installed. E.g. ""
Unattended-Upgrade::Mail "root";

// Set this value to "true" to get emails only on errors. Default
// is to always send a mail if Unattended-Upgrade::Mail is set
Unattended-Upgrade::MailOnlyOnError "true";

// Do automatic removal of new unused dependencies after the upgrade
// (equivalent to apt-get autoremove)
//Unattended-Upgrade::Remove-Unused-Dependencies "false";

// Automatically reboot *WITHOUT CONFIRMATION* if a 
// the file /var/run/reboot-required is found after the upgrade 
Unattended-Upgrade::Automatic-Reboot "true";

// Use apt bandwidth limit feature, this example limits the download
// speed to 70kb/sec
//Acquire::http::Dl-Limit "70";

As you can see Automatic-Reboot is true and thus the server should automaticly reboot. Last time I checked the server was online for over 100 days, which means that the update from Debian 7.1 to Debian 7.2 has happened while the server was up (and indeed, all updates were installed), but this involves kernel updates, which means that the server should reboot. It did not. The server was running very slow, so I rebooted which fixed that.

I did some research and found out that unattended-upgrades responds to the reboot-required file in /var/run/. I touched this file and waited one week, the file still exists and the server did not reboot. So I think that unattended-uppgrades ignores the auto-reboot part. So, am I doing somthing wrong here? Why did the server not restart?

The upgrade part works perfect by the way, its just the reboot part that does not seem to work as it should.

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do you have molly-guard installed? This programm can block automatic reboot… – ThorstenS Nov 8 '13 at 10:45
I do not have molly-guard installed. – Cheiron Nov 8 '13 at 12:32

The file /var/run/reboot-required the configuration talks about is created by a script in the package update-notifier-common. Without this package installed, no automatic reboots are going to happen.

Unfortunately, this isn't mentioned anywhere in unattended-upgrades!

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