Did you insert the document in a skewed way into the manual feeder?
When you insert a document into the manual feeder to perform a scan, insert it straight into the middle of the manual feeder.
To not display the message even though a document is inserted skewed, clear the [Scanning will not start if the inserted document is skewed] checkbox in the scan settings in the following procedure.
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Display the scan window of ScanSnap Home on the computer.
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Select the profile that you are using from the profile list.
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Click the [Edit profiles] button to display the [Edit profiles] window.
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Click the [Option] button for [Manual Feeder] in [Feed mode setting] to display the [Feed option] window.
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Clear the [Scanning will not start if the inserted document is skewed] checkbox.