Hi Milos,
I pretty much keep the default settings but usually set the image overlapp to high (as I have a pretty high overlap) and sometimes provide a prior focal lenght estimation. The problem seems to be that at one point it just stops extracting tie points for the images (and therefore also skips the rest of the procedure). The images where the tie points are detected are consecutive, but not necessarily at the beginning or the end of the imput images.
Cheers,
Jo