|Appeared in:|| WALL•E|
That may imply that the computer just didn't have the authorization to affect the autopilot but that does not mean that the computer was not responsible to waking up the other robots on the starliner when they were needed.
When the computer's inability to affect AUTO is noticed, it may first seems that the computer was only a reference database and had no any actual control over the starliner, but some details clearly show that that is not the case. So it is unknown if the computer could truly affect robots.
When AUTO was turned off it was the computer that made the Axiom to hyper jump and return on Earth. Also when the captain pushed the green button it is likely that computer closed the doors of the bridge and presented the message from Shelby Forthright about the Operation Recolonize. It is also clear that it was the computer who opened EVEs cavity to receive the plant after captain has "allowed" that to happen. The computer also seem to have the control over the escape pods and the probe ship.
These points clearly indicate that it was really the computer who ran most of the functions of the Axiom and that AUTO was responsible for piloting the starliner, but it seems that he had domination over the computer since he was able to disconnect it from captain's quarter, and that was why the captain was unable to order the computer to let him out of the room.
The computer is even more programming-based than AUTO, but has a more human-like voice than AUTO has. The computer only acted in specific, pre-programmed situations.