I have noticed that certain sets of nodes appear to be non-deterministic in terms of their layouts. For instance, the test set
SugiyamaTester13.gml constantly changes (or actually alternates between a few) layouts when the "Relayout" button is repeatedly pressed.
I'm not sure, as I don't totally follow the math, but I didn't think there was supposed to be non-determinism in the algorithm. Perhaps someone smarter than I am can enlighten me.
I'm not sure this is a bug... but it kind of feels like one...