someting that you can quickly try if you haven't all ready is to Clean the small strip of glass to the left of main copying glass. Sometimes toner, white out, or even a little smudge will casue the lines that you are talking about.
When you use your top document feeder, this is what actually scans your documents. Even the smallest of smudges or even a black dot will create lines on your scans and copies.
It could also be something else, just thought that this would be a good thing to try.