In the meanwhile I've been testing a bit. I've created a new sequence, and used extreme dithering and a 5 second settle time as settings in SGP. In PHD I still have selected spiral dithering. Now when I start the sequence. I've also set these settings in another, older, sequence. I've been running these sequences and I see dithering happening in PHD, in the graph log, and I don't see it in the other. So it seems to be a problem with the older sequence.
So I've recreated the older sequence and now all seems to be working fine again .