To update my last post, this solution worked for me:

On the Slideshow2 homepage is an working example with vertical alignment. So I downloaded exactly  this version of the slideshow2.js and the according mootools and tadaa! It works. It seems that the current version simply is not capable of vertical scrolling.

A single drawback is still there: The option “resize” doesn’t work. But as long as you can live with that, the slideshow2 V1.2.5.1 is sufficient