Update: I found the culprit!
I think it has something to do with the Layer Height Limits in the Printer Settings tab and the contact Z distance of 0.05 I was using. Changing the distance to 0.1 resolved the issue.
It would be nice if there was a warning somewhere that the two settings affect each other or at least some hint that the support couldn´t be generated correctly. It messed up at least two long prints until I found out what was going on.