I noticed when I was playing contra on the first level all was good. The top screen was like a few pixicals above the medals. Once i got to waterfall level that moved way up. After I beat it, I checked the the settings and both vert borders and the colors and defaulted but nothing else. I've noticed it a few times but this is the first time I saw it in the middle of game play. Any ideas?

Sounds like that is just how the game works. The waterfall level is vertical so the game uses more of the screen in that stage.

Watch this video, is that what you are seeing?

It is but why would it reset the vert border and the color palette in my avs settings? Just kinda confused is all