It's clarified in 2010. ...Instead, it builds up like a psychosis in his subconscious. As the mission progresses and the flight crew become more curious about the circumstances of their mission, he's trapped in a mental maze of increasingly constricted pathways, until eventually he's led down to the one path that is open to him.
The only way that he can keep the mission secret without lying to the flight crew is if the flight crew no longer exists.
Sounds like the computer version of a Freudian serial killer excuse. It may be an explanation for why he's malicious, but it doesn't change the fact that he's malicious.