"so I connected the motherboard to one of my other DS´s top screen and the problem is still there! It also isn´t the 3D chip on my DS that is the problem, because if I play Zelda Phantom Hourglass, which has the 3D image on the bottom screen it just shows normal images. But whenever I go to the map and the 3D image goes to the top screen the textures and colors again look strange."
Sounds like it's the 3D chip afterall?