Ah! I have a mold problem too! I have no idea what to do =(
Is it mold or is it dissolved salts forming as the water evaporates?
I dry a lot of stuff slowly, under plastic in the humidity of Atlanta and have not seen this on Masonite bats. It may be something from your clay body. Try cleaning the bats very well in straight vinegar.
Thanks for the suggestions. I'll try the vinegar. I'm leaning towards the salt and mold theory. I think it might be standard mold that is colored by salts or soluble elements in the Masonite glue. It is an amazing color for mold.