Is [Normal] selected for the image quality level in the scan settings?
Try scanning again after making the image quality level higher in the following procedure:
On the touch panel of the ScanSnap, select the profile that you are using from the profile list in the home screen.
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Press the image quality level setting icon to change the image quality level.
Example: [Normal] → [Best]
If you change the scan settings on the touch panel and scan a document, after it is scanned, the scan settings will return back to the settings before any changes are made. If you want to scan documents under the same settings all the time, the scan settings need to be saved as a profile.