This is not a particular behavior of 2.5 beta nor of 2.5 alpha but - as far as I remember - of any previous Autopano versions...
Georges, that hasn't been my experience. I tested the same images in APG 2.0.9.
Here is the behavior in APG 2.0.9.
1. Groups: Load 6 landscape images.
2. Detection set to Fisheye (see screenshot)
Result: Horizon is reasonably straight.
4. In CP editor, remove CPs from clouds.
Result: Horizon is straighter.
6. CP Editor: add a few more control points along land/sky margin.
Result: Horizon is very straight.
However, I will agree with you on one point about snapping to zenith.
In APG 2.0.9:
1. I manually pulled the pano out of alignment so it resembled the roller-coaster horizon in the second example the set in my previous post.
2. Clicked on 'automatic horizon'.
Result: The zenith snapped to the center point.
I don't think that part is unexpected behaviour, because the zenith is probably the position closest to the previous horizontal/vertical axis.
Mac Pro Quad Core Intel Xeon
Mac OS 10.6.4