This is a REALLY good post, RalfH!! I am having the similar issue with Photoscan Pro. If you remember the posts I had before, we have a camera setup for taking images for small plants, and the overlap between images are more than 50%.
But the "Align camera" seems to be a little strange to me, that is some time Photoscan can't align images together (the positions are completed wrong), but with the same set of images, Photoscan can align them perfect 2nd time, but it might not be good for 3rd time....
This issue happened to me a lot and seems to be "random". So I really want to know what is causing it and how to fix it.
Nan