I think what's happening is that you're breaking up the charcoal with the brushing on
of the second layer.
Your bits of charcoal had just been dropped onto
the first layer, right, and basically left alone (so they'd mostly be stuck to and in the clear finish), but adding the second layer meant the charcoal got pushed around, I'm assuming, during application so it broke up into finer powder? (Some other white "mediums" probably wouldn't break apart so easily.)
Here are some suggestions for powdered sugar from my Miniatures
page, in the Foods section:
...for very thin icing with areas of whiteness... I buy white charcoal sticks from the art store (near the black charcoal)... you could also use a hard white dry pastel pencil or stick
......I just dab a little TLS liquid clay on the surface of the food, grate the charcoal with a razor blade, and then bake... if some comes off (which it will), after you glaze/varnish it just throw on some powdered charcoal while it's wet
.....Nora Jean scraped bits from a white pastel pencil with an Xacto onto her jelly-filled donut...had rubbed liquid clay there to hold them on, then rebaked
........other sticky surfaces to hold the sugar could be white glue, a clear acrylic finish, glycerin, wet paint, etc, all of which would dry, not have to be curedhttp://www.norajean.com/Food/Donut/JellyFilled-008.htm
......or could try white chalk scrapings ...other white powders (drop them from a seive to keep from clumping?).... or white embossing powder (heated)
......iampoison used scrapings from white charcoal stick for drawing
......or "spray" dots of white acrylic paint onto the top area with a toothbrush... could mask areas where don't want speckling
(there are also suggestions for making faux granulated
sugar on that same page, if you're interested:http://www.glassattic.com/polymer/miniatures.htm
....click on Donuts, etc.