Thanks for the detailed description there and the video. I see what you're talking about.
It looks to me as if youre stencil has many semi-transparent areas. The way Artrage works, these allow a certain percentage of the media's full opacity through. When you move the stencil, you're essentially resetting that and doing it again. We make sure that the threshold is set until you move the stencil. Currently there's not a way to ensure that that threshold is remembered when the stencil is moved and previous media is overlapped.