@Sphere: I think Decker says something about a faulty backup crystal in the transporter circuit right before Kirk comes to relieve him. Seems like that might be a part of a failsafe system.
"The transporter circuit was not activated. Faulty module."
I can only imagine what the transporter's computer system must have been thinking. "What the Hell do you want me to do?! I don't have any brains damn you!"