Ooops, I've taken a deeper look and I'm pretty sure it's not a build bug but a bad table setting. (Remember I'm not modder at all)
The Amadeus-Class seems to have incoherent table entries:
$Name: Amadeus-class
...
$Max Velocity: 0.0, 0.0, 25.0
...
$Max Oclk Speed: 23.0
So, reading what Wiki says, an Amadeus class transport goes faster at normal engine energy settings than at maximum settings
...
It seems that the new Autopilot code makes you travel at the slowest $Max Velocity of all set-nav-carry ships. But with the original ship.tbl, you are actually travelling faster than Aurora capabilities. (Maybe old autopilot code took the MIN between both $Max Velocity and $Max Oclk Speed, so it hid this table error).
I've swapped $Max Velocity (23.0) and $Max Oclk Speed (25.0) and then it runs fine. With these new settings, what happens in this mission is:
+ At the beginning, Aurora is flying at 15 because of the cap-waypoint-speed SEXP.
+ When Aurora recieves the cap-waypoint-speed = -1 SEXP, it accelerates till 25.0.
+ Then, you initiate the autopilot run and every single ship travels at 23.0.
I upload a patch table, but please fix it in the final WCS release.
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