I just wanted to update this thread so that others can know what the issue was. Fanuc got back to me finally after looking at my backup, and here is their response:
"Our investigation has concluded that your robot is loaded with the enhanced stopping option which is also known as a Stop Pattern type B. enhanced Stopping option J692 option installed. Which from what I see in the DCS manual means all stops whether initiated by Controlled stop or estop are treated as full power off stop. This option will require a re-burn of software to remove."
So it is an option for the robots apparently. Hope this can help others with the same issue!