I found the reason for the artefacts/seams: It is related to another problem, that I have already posted here:
http://forum.allegorithmic.com/index.php/topic,986.msg4097.html#msg4097for some reason, substance painter sometimes gives me a very low resolution, no matter what document size I have. If so, you get the seams due to the fact that there is not enough resolution to sample/paint the pixels at the geometry borders.
Again for some reason, and after a lot of crashes, I got the resolution problem solved, which also made the seams disappear.
I am not able to analyze the problem, as painter crashes especially upon importing meshes and maps, and saving and opening files.
Still I was able to save a custom project, and as long as I only paint and save, Painter stays stable.