Hi Try to scan by using the quick menu as I described below:
Check for the ScanSnap Manager icon on the taskbar.
Right click the mouse button over that ScanSnap Manager icon.
Select "Scan Button Settings" from the Right-Click Menu.
Select the "Use Quick Menu" check box (it must be checked).
Load the document in the ScanSnap which you want to scan.
Pres the "scan" button on the ScanSnap.
Click the "Scan to folder" icon in the quick menu when scanning is completed.
The "Scan to Folder" dialog box appears.
Check the scanned image in the "Scan to Folder" dialog box.
By clicking save buton, save the scanned data in a specified folder which you select chancing the filename as you want.
Hope this helps.
Please post your feedback and Vote if the problem resolved as per your satisfaction.
I got off the phone with Fujitsu and i was told you need to make sure that the ScanSnap Icon is in the system tray without a Red Line cross through it, so if it is not in your system tray start the snap scan program, if it's disabled re-enable it and you should be good.