Ok, I am FAR from a photography expert, but I think the topdown box will only help with clarity. The flash is definitely the problem in those photos above, keeping the colors from looking like they should. I can tell that you have a bunch of beautiful and colorful corals, but looking at those psychedelic photos makes me a little woozy!

Our cheap point and shoot camera (Nikon S550) has the option of choosing different flash settings, to include a night-time flash and no flash, etc. Look for that option and play with your flash settings for different results.