probly you are using a photocopy as scanner what make a big diference. I had this problem with my scans too, trying to stel some machines in my job when i use the properly scan i get it right, when use the photocopy to get it, i have the same of your result.
I guess that you can changes the configuration of your scanner (if it is a photocopy like i do) i change the resolution and create a TIFF file, sometimes it clean all my image copied.