I have the same issue with my scanner. I guess that's just how scanners are--- they mess up the artwork. I have never found adjusting the scanner's settings to be helpful though. I have, however, learned that the best way to solve this issue is to edit the image in photoshop. What I do is that I hold up my illustration next to my monitor and I try to tweak the Color Balance, Contrast, Vibrance, and sometimes, Curves until the image on display is similar to the one I'm holding. You'll need to do a lot of trial and error with this process but you will get there. There is no fixed way to go with this. It all boils down to how you feel about the image. I hope this helps.