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Just off the top of my head some things you may have over looked.
1 Are your darks current? ie less than 3 months.
2. in CCDstack check to see if you have time scaled checked on your calibration with regard to darks. ie if you have a 20 minute dark and applying that to a 10 minute light you can get dark blotches. Or if you have the correct length of both dark and light you might have the time scaling set it can cause this too. Easy to over look.
Also just check to see if data rejection set correctly. Under correction can cause stuff to slip through. Though in the case I don't think this is the problem.
Like others have said it is hard to determine what is going on from that cropped image and at what scale.
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