I put it in my dropbox. Watching it again, it seems to only happen to the cylinders and cubes. I also noticed it while playing Urban Champion just now. It seems to be that when 2 sprites occupy the same spot and you try to change one to a cube/cylinder, the 8x8 tile of the sprite you are changing disappears. In the Punch-Out video, there is a white sprite that you can't really see because of the see through effect you get while editing. But it would be in the same spot as the sprite that keeps disappearing.
I will investigate it later
Now that I know, I have noticed it more in other games, too. Urban Champion and Dig Dug were some I was playing with and I can reproduce it pretty easily. It definitely is happening during sprite overlap.