Comment 5 for bug 178775

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.