Are you sure that you selected the correct profile that you want to use for scanning?
Since a different save destination is specified in each profile, if a wrong profile is selected for a scan, scanned images may be saved in an unexpected save destination.
In the home screen on the touch panel, check whether you selected the correct profile that you want to use for scanning.
You can check content data records created from documents that you recently scanned by selecting [Recent scans] under [Scan history] in the folder list view on the main window.
If necessary, move content data records to appropriate folders.
For details about how to move content data records, refer to ScanSnap Help.