Hi
I think a few others have reported a similar issue before, here and at Polycount. I think those involved Polypaint though. This involves painting/adding a different material to certain sections. Either way, the issue is linked to using Layers. Baking them down fixes the issue, but it would be awesome if this issue was fixed. 
The plan for my project was to use a Layer to sculpt muscles of the face and then paint a different material over them. The problem is is it shows everything in black instead.
I know the image looks like I have RGB enabled, but it’s because I have to hold down Ctrl, Shift and Print Screen to take a snapshot. Only Mat is enabled for the brush though.