Just did the 2016-003 security update and I'm pretty sure it also did a firmware update of some sort. After the screen went black to reboot there was a loud beep followed by an odd reboot screen (wrong resolution) followed by several other restarts. After it was done, things seemed to be in an odd state (not unusual for Apple these days) so I rebooted. After the reboot I found that I had been booted into my backup disk image rather than the one on my main disk! I reset the startup disk to the main disk, and the reboot worked correctly this time. QC, we don't need no steekin' QC. (New catch-phrase, replacing "It just works.") Also, it would be nice if they'd alert you when an update was more than just a software update.