EdSet100,
There's quite a difference between an SAS and an Autopilot.
The MRA4 issue is, as I understand it, poor handling qualities in pitch. This is being fixed via a new full authority pitch stab system ( a bit more involved than a traditional SAS). Once that is sorted, the autopilot system has a chance to work.
The issue of how long this was known about is a good one to raise, though. I've been told that it was raised as an issue early on, but pushed to one side as the team struggled to get the project to fit within the (original) price the BAES managers had agreed with the MoD.
This could turn out to be a classic example of saving ten quid up front to spend a few hundred downstream...only add a few noughts on.
Be interesting to see whether this one ever gets fully investigated in public - don't hold your breath...