The application may be removed from Login Items for some reason.
Follow the steps below to add ScanSnap Manager to Login Items.
[Workaround]
Add ScanSnap Manager to Login Items as follows:
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Select [System Preferences] in [Apple] menu.
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Select [Users & Groups].
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Click the current user name.
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Click the [Login Items] button.
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Click the [+] button.
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Open [Applications] folder and select [ScanSnap] > [ScanSnap Manager].