How do I fix the scaling problem with Dr. Lunatic SWC? I keep trying to make the game fit the screen but nothing is making that happen. Please help.

I realize this post is from half a year ago, but in case you're still interested, SpaceManiac's version fixes this issue, though it's a little more tedious to get up and running. When you get to the final step, remember to type "./run supreme --fullscreen" (without the quotes).
https://github.com/SpaceManiac/HamSandwich