Hidden Sprites and Color Issues

Hello everyone.  I hope I'm not asking a question that has already been answered in the forum somewhere. But, I haven't been able to find it. In fact, Ive been unable to find my problem addressed anywhere online. But, I digress. Getting right to the matter, I've been using various tile viewing/editing utilities (namely Tile molester , TilEd2002 and a few others), and I find that there are certain images that never appear in the lineup. Or, if they do, they are so horribly jumbled as to be unworkable. I've tried looking through different codecs, but with no success. My second problem is exclusive to Gameboy Color and NeoGeo Pocket (more so NeoGeo). There are certain images that contain more than four colors, but the color pallet never exceeds four. The images appear in the sprite list as undetailed shapes. I suspect that the second problem might be related to the first in the form of an additional overlay image that is not showing up. The Sprite ripping utility in Visualboy Advance Has helped to some degree with these two problems, but it only allows me to find hidden sprites/pallets for Gameboy/Advance titles. NES, SNES, Sega, etc... If anyone can offer a solution I'd greatly appreciate it.