Some scanners use a sliding shutter (basically just a white backing) that travels under the glass with the scanning arm, to prevent reflections below from being picked up as part of the scan. You might want to take a closer look at the traveling scanner arm to see if the backing has gotten itself disconnected somehow, and is getting left behind when the scanning arm traverses the document.
If that doesn't sound likely, post a sample image here.
What model of scanner are you using?
