I wonder if there’s a correlation between your dark spots and the yellow ones I had on my Gouda. They were bright yellow at first, and are now faded to a dull yellow. They have not spread or increased in size, and cannot be removed with brine wiping. I have another unwaxed cheese, a Montasio, near it and it is not affected. I’ll be waxing the Gouda tomorrow, and I think I’ll scrape the spots a bit and see if I can get rid of them. They may be harmless, but I don’t want to take the chance. If you have a revelation let us know.