Did you load the document in a skewed way?
Load the document straight in the ADF paper chute (cover).
To not display the message even though a document is loaded skewed, disable the function for detecting a skewed document 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 [Feed] to display the [Feed option] window.
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Clear the [Detects a skewed document to protect the document] checkbox.