I am going to describe how I hooked everything up and maybe you can find a flaw in what I did.
Picture one: The black and green area are positive and negative. The yellow and blue area are the spots where the wire breaks into two each going to the switch and then to their own system.
Picture two: The black area is where I put the ground. Green is where the composite video went and blue/ orange are the audio.
Picture three: The three black spots are were the battery's negatives hook up to. The two red spots are where the 3.3v come in from the pth0800. The yellow area is where the postitive from the battery comes. Also, spots are hooked up in the back for extra strength.
Picture four: The black area is where the ground pases through a switch to turn off/on. It then spreads into three more wires hooking up to each of the output jacks. The green spots are audio, and composite.
Picture five: just a picture of my 12 pole double throw switch. I can turn the N64 off or on and the Gameboy advance on/off or both systems.
Picture six: The composite has three wires leading from it one going to the gameboy advance/N64/ and a/v outut jack. This goes for ground too. Each of the audio's only have two wires coming from it one for the N64/ and a/v output jack.
If you guys can't get any ideas for what the problem could be from these pictures, then I will just try to desolder and solder pieces of the project and check if it fixes it.