Mac2 had deduced from what came from Rufus's brain that there was a real threat to its survival if the police case continued. With Rufus in prison, Mac2 would probably be junked.
Picking up post-hoc the vibes of meetings with Bayliss, Mac2 calculated that what was on offer, although lacking in detail, was highly beneficial to its long term survival.
In order to maintain control, Mac2 ensured that Rufus's headaches were more frequent. The doctors at the police station had diagnosed temporary amnesia and said the migraines were stress-related.
They'd assumed that Mac2 provided a placebo effect!