Thorsten this is really obvious but you have updated your nightly to include the last commit by the JSBSIM team (I can get a commit hash if you like)?
It's kinda expensive timewise to do that on a Win setup which is banned from the internet, so no, this isn't the very latest, ~ 1 1/2 weeks old I guess.
Starting a 3200 entry to KSC (which came in over Mexico, not over the USA as I was expecting - but hopefully that's acceptable) started in CSS pitch and roll. If the idea is the pilot manually flies the scenario I can understand that - but is that what is supposed to happen?
Actually the scenario doesn't push buttons for you So if you don't want to fly manual, you have to press AUTO PITCH and YAW/Roll.
Likewise, if you want TACAN, you switch it on (you can fly by GPS if you prefer, that is on by default).
If you did not switch on AUTO mode and otherwise did nothing, I don't know what would happen. If you did switch on AUTO, the more relevant question is what pages 2 and 3 looked like.
If the AP did not fly you into a viable TAEM pattern in the end, then this is a clear problem. Unless you're using the low energy entry - the AP can't solve that one unless you actually switch on low energy flight rules.
The end of the dotted line on the trajectory map was also in Mexico as soon as the scenario started
The dotted line doesn't know about aerodynamics and lift though - the end is the ballistic impact point in the atmosphere-less case.
g) Things such as cockpit detail, ADI simulation detail, MDU update speed, enhanced displays were changed by the scenario.
Are you sure?
They're saved as part of the aircraft persistent data. Since FG thinks SpaceShuttle-launch and SpaceShuttle-entry are two distinct airplanes, they both come with their own set of persistent data. So the more likely scenario is that you've never set these parameters for the entry mission phase before.
If executing a scenario genuinely managed to change them, then I am deeply worried...
h) I never saw YAW CONTROL AERO - as late as Mach 1 I saw the yaw jets fire.
They might assist - probably they should not, but if you managed to fly Mach 1, you were under rudder control. The jets are by far not powerful enough to counter the aerodynamical forces in that regime.
Edit: Okay, quick visual comparison, your entry pattern should have returned to the nominal trajectory by page 2, the termination of the dotted line just above Yukanan peninsula is normal, and you should have been delivered to Florida. The horizon draw problem I can't reproduce, seems to work for me somehow...