my guess is that the state vector is slightly off at the end of TAEM
It is, but by not much; I am always compensating by the same shift I see between the real runway and the hud (TACAN and Air Data in the state vector, MLS works as expected). Something else seems to be going on!
I have tested 3 landings, TAEM scenario, with Navigation=Perfect now, and I've let the AP doing the HAC for me. The wind was 0 knot.
For 3/4 of the HAC, the circle predictors on SPEC 50 are always significantly outside the circle, so the AP does not seem to follow the SPEC 50 circle. But, in the last 1/4, they are significantly inside, as if the AP was trying to compensate later on. At all times, the diamond tracking remains good, most of the time inside the cage. Therefore, it looks like the diamond does not match the HAC drawn on SPEC50? At last, when the AP force me to take CSS on final, I am completely off the runway, the runway is on my left. And the final is far too fast, I am still arriving over the runway at more than 320 knots, as if I had a 30 knots wind from my back (and speed brake retracting).
Other very weird things I've observed. In the "fly-by" view, within the HAC, it looks like the sideslip angle (beta?) is also completely off. The nose of the Shuttle points well outside the trajectory, it looks like it flies the HAC while crabbing outside. And also, on the runway, I have to push the rudder quite a lot to the right, as if some crosswinds were present. I have checked a few times, the live weather reports 0 knot, and my joysticks are all trimmed to a good 0.00.
On the other hand, for the Shuttle-approach scenario at KTTS, everything seem to work fine! I am a bit lost :-/
Edit: On the bright side, I am getting exactly the same behaviour with Milestone-12, so none of your changes are the culprit here!