I ran some Apple updates last night. One of the updated included an update for the MacPro firmware. Thus began the fun.
It said to close all other applications and then use the "Shut Down" button in that window. It said to, after it powered down, press the power button until the service light blinked or a long chime sounded. I assumed that it meant the startup chime. I was wrong.
For all of you out there that will ever upgrade your Mac's firmware, hold the power button down. It takes about 5-10 seconds for it to happen, but the service light will blink and the long, single note chime will sound.
The only difference I've noticed so far is that my problems with ejecting discs have stopped. That's a good thing.