easiest way to get rid of the archiving on the square images is to turn off anti-aliasing before you draw the box. photoshop is trying anti-alias the edges of your image to make it look "smoother". this works best for squares and lines, not rounded items.
don't bother saving your images as .tga's either. save them as .png's and import them into skinstudio. skinstudio will convert it to a .tga for you.