I just had a similar problem when I replaced my computer last week. Before, I would scan an item and it would be saved under 'My Documents'... After I reinstalled the scanner software, I would scan an item and it disappeared. Checked in 'My Documents' folder and it wasn't there... SO, I checked the scan save settings, and found where the scans were being saved to. At that point, I changed the save settings by clicking on the browse button and clicked on 'My Documents' folder. Now things are getting back to where they were before.

Hope that helps.