Dave,
Little black spots?! Hell, you should see the little shelf fungus growing out of the centerboard case logs on my dingy. Probably shouldn't have used that pallet ash. Your blocks have something taking nourishment from them and leaving their telltale stain. wood mold spores are everywhere. All they need to is air, moisture above 50% and temperatures above 70deg. F. to thrive. So your blocks were either pretty moist when you encapsulated them or are getting sufficient moisture through the encapsulation. Epoxy preserves wood by slowing the moisture exchange needed by these little fellows.

I'd give then a couple coats of epoxy and watch them to see if they get any more or bigger spots. If the spots bother you, tear them out and replace them.
Good Luck,
Geo C.