Apache doesn't run when using shutdown -r, does when using reboot

I've uncovered the reason why I can't reboot my web server sometimes without apache2 automatically starting after boot.

If I run reboot now Apache comes up fine after booting. If I run sudo shutdown -r now, it doesn't and I have to manually SSH back in and apachectl start.

Is there some difference between the two commands that would cause this?

Ubuntu 14.04.04 LTS with latest updates and dist-upgrade on an SSD-based VPS.