Last year I had some late season chrysalises that formed black spots very similar to yours. They showed up about 1 or 2 days before the butterfly was preparing to eclose. All of the butterflies eclosed normally, had no problem hanging and flying away. Also their abdomens were pretty clean looking.

All of these signs does not mean they didn't have a mild OE infection. I didn't worry too much because it was late season (September) and if these butterflies were infected, I figured they wouldn't make it to Mexico or very far in their migration before they expired. This could be faulty logic?

Anyway, I just purchased a small microscope, so I can find out for myself if it happens again!

Can you post another picture? The one posted is blurry, so it is hard to see the spots. If the spots are under the cuticle of the chrysalis then it is very possible it is OE. If it is on the surface, then it is something else. Sometimes there is an injury to the chrysalis (like when another caterpillar walks over it) and it can be dark as well. Dark spots in general can be lots of things. Often it is melanin produced in response to a pathogen (bacteria, virus, etc.) or injury. OE is one of the few pathogens that the dark spots are actually the spores.

Once the butterfly emerges (if it emerges)the spores are then on the outside of the insect on the scales. The spores are large enough to be seen by microscope.

Hope that helps,
Elisabeth