EJG;
There are a number of things that can result in those black spots, reduced iron particles (iron in the enrichment blend in the flour “enriched flour”), or they may also be due to yeast agglomerates, possibly due to use of ady that has not been pre-hydrated, you can discount this if you are pre-hydrating the ADY. It can also be a reaction with the bran particles in the flour too. Normally, a light coating of salad oil on the dough balls after they are placed into the dough box is all that is needed to prevent the black spots from appearing. They are not harmful, and yes, they do disappear during baking.
Tom Lehmann/The Dough Doctor