I decided to do some experimenting. I formatted the SD card and put a fresh 4.4 install on it. I updated the RetroPie scripts and then copied the splash screen to the appropriate directory on the SD card. There was nothing else done to the system.
Even with this configuration I can reproduce the problem although it appears to be a timing issue.
If I try to restart the system within 5 seconds of emulation station starting it always displays that error. This sometimes happens between 5 to 10 seconds as well. It can also happen (although not as often) if I begin the restart process (Start, Quit, Restart System, Really Restart?) but don't click "Really Restart?" right away. I can let the system sit for 20 or more seconds and when I do confirm the restart it will happen.
I need to re-image my SD card with my last backup to see if these times are extended by making changes in other areas.