Hi Geert,
I have just made several tests on Linux and Windows, and StarAlignment works fine.
Meridian flips are no problem at all with SA. However, if you have mirrored images, you have to select triangle similarity instead of polygons as star matching descriptors (triangle similarity is selected by default on the BatchPreprocessing script). Anyway, this cannot be the cause of the problem you are seeing. Can you try with a different data set?