Try the following procedure on the [Scanning mode option] of ScanSnap Manager.
By sliding the bar on [Brightness (Black and White scanning only)], you can adjust the brightness from 11 levels. The scanning result will be blighter if you slide the bar to left, and will be darker if you slide the bar to the right considering the center is the standard.
Select [Setting for text only document] check box before scanning.
(By selecting this check box will emphasize the lightening of the image data.)