Hm. I scan at 200 DPI as well, with an HP Scanjet. But, my colored pencils still come out a bit muddled until I adjust the noise and resize the image. I'll need to play around, it may be my paper quality, too, as I use a smooth texture. Perhaps if I color on a rougher texture, it may hold the colors better...
When you layer on colors, do you have any underlying sketching aside from the linework, like any light monochrome shading? Or do you just go right to the coloring? I start with a monochrome shading for reference, then start layering. Perhaps it's my methods, or even the brand of pencils I use. Hm, I'll need to play around and see what works best with the scanner...