The problem appears to be that interfaces that are not marked auto in 
/etc/network/interfaces will not be touched by various system scripts and 
NetworkManager will not touch them either. From /etc/init.d/networking :
            if ifup -a; then
                log_action_end_msg $?
            else
                log_action_end_msg $?
            fi

>From the ifup manpage -a means "affect all interfaces marked auto."

If you look at udev rules you can see something similar. From 
/etc/udev/rules.d/85-ifupdown.rules :
ACTION=="add",          RUN+="/sbin/start-stop-daemon --start --background 
--pidfile /var/run/network/bogus --startas /sbin/ifup -- --allow auto 
$env{INTERFACE}"
--allow auto is effectively only allowing interfaces in the auto class which 
appears to be similar to -a .

If a user manually does ifup <interfacename> then the interface appears
to be brought up and configured correctly.

Now either NetworkManger needs to be taught to configure static/manual
interfaces that lack auto ( which apparently does for Fedora
http://bugzilla.gnome.org/show_bug.cgi?id=518189 ) or whatever is
writing  /etc/network/interfaces (often gnome-system-tools ) needs to
add auto to interfaces when they are configured manually. Until this is
done manual/static interfaces will continue to be broken on boot.

-- 
Can't set static IP  --network manager--
https://bugs.launchpad.net/bugs/178775
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