Just to duck back into the conversation, let me be as clear as possible about what happens to me. The black areas appear around the edges of my created scenery where it is overlaying areas of default scenery. It is NOT inside the center of the new areas which also, of course, is overlaying default scenery, but only on the edges where the new scenery is overlaying default scenery. It doesn't do this everywhere that the edge of the new created scenery is found, only in select areas. It is NOT present where new scenery butts against or covers other newly created scenery. That is where I get a strip of very low resolution scenery, and I can live with that.
The problem seems to me to be a conflict between the new scenery's edges and the existing default scenery. So, if you created a huge scenery area and only flew near the center, you would likely never notice it. As an example, I created an area that spans from just west of Pittsburg to the edge of the decent default scenery east of Chicago, stretching about two degrees in latitude. The black areas occur over the great lakes, and interestingly show up as white when they are over water.
I also created a single scenery from east of Innsbruck to Vienna. This time the black area shows up where the scenery ends just east of Vienna.
Now, just to confuse things, I created an area from Boston to where the NEUSA DLC stops providing crisp ground scenery, just east of Hartford. That area produced no black areas that I have found.
So it's clear as mud! I have no idea why some areas do this and others don't, but this is as detailed a description as I can give you of what is happening.