Are you sure that you selected the correct profile that you want to use for scanning?
When scanning a document, if you select a wrong profile, scanning does not proceed with the expected scan settings.
In the scan window of ScanSnap Home, check whether you selected the correct profile that you want to use for scanning.
The document type for the scanned document may be detected incorrectly
When you scan a document with a profile that is configured to detect a document type automatically, the document type for the scanned document may be detected incorrectly.
Select an appropriate document type for [Document type detection] in the [Edit profiles] window and perform a scan.
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You can change the document type for a content data record after scanning is complete.
For details, refer to ScanSnap Help.