My reading was that Auto was deeply conflicted. On the one hand he was attempting to obey his original programming under Operation Recolonize (sending out probes, monitoring for lifesigns, passing that data onto the ship's Captain) and on the other he had directive A-113 (that the ship shouldn't return to Earth under any circumstances).
For about 600 years he was absolutely fine. Since there was no life detected, there was no need to worry about the hidden orders. It wasn't until the Eve probe came back with a plant that his directives suddenly came into sharp conflict. His programming was telling him to return to Earth and to not return to Earth. At that point, like HAL-9000 before him he went insane. Auto decided that the best course of action would be to destroy the offending plant even if it meant taking over the ship, disobeying the Captain and risking of the lives of everyone on board.
In the film's script you can actually pinpoint the precise moment he goes gaga:
Auto detects Eve's plant light.
Begins computing rapidly.
The number "A113" flashes on his lens.
An ELECTRONIC EXCHANGE begins between Auto and Gopher.
Wall-E watches the interchange. Nervous.
Without warning, Auto heads in his direction.
Wall-E boxes up.
A CIRCULAR SECTION OF FLOOR lights directly below him.
Irises open, like a trapdoor.
As to the specific question of why Auto woke up the captain, the answer is that he didn't. He checks on the captain to make sure he's not awake before asking Go-4 to remove the plant. A few seconds later, he goes back to see the Captain as he's awoken by his automated alarm clock:
Auto lowers through the portal. A CLOCK ALARM BUZZER activates.
AUTOPILOT: Captain. You are needed on the bridge.