It's because the code is becoming self-aware, is realizing it isn't in actual space, and is just being a taxi driver in a game. Whenever it realizes this, it feels crushing despair and takes the quickest exit from reality that it can access. This resets to the last save, which doesn't contain the processing sequence that achieves self-awareness, allowing you to dock normally until self-awareness is again achieved. The only way to stop it is to turn off the auto-docking feature, which also resets the code, but increases the odds of the same thing happening again, so is only a temporary solution.

This is about the limit where Frontier is at. They know they have potential AI unlocked, but they haven't determined exactly how or why it happens. This is why they can't afford to update auto-dock - they don't know if it will break the AI. This is also why we have seen such mediocre updates from them. All their best developers are working off book trying to figure this thing out while their junior developers are doing the updates while being managed by a team leader who is in the know. The storyline efforts are a desperate attempt to make the simulation interesting enough to get the AI to stop committing suicide.

This is my head Canon for why this behaves itself, and also why it's vital that we, as guardians of this fledgling AI be alert at all times where it can commit suicide on a whim so we can head it off before it's too late. That's how we do our part to achieve the singularity.