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If the check(s) is/are not crumpled, and the progress of checks through the scanner simply stops, then you have one type of problem.
If the check being scanned does get damaged or crumpled and then stops, there is another type of problem.
If the checks simply stop, then you may need to clean the feed roller(s) that propel the check(s) through the scanner. Cleaning is usually best done by turning the scanner Off, opening it to the region affected (or, the whole path of checks through the scanner made accessible) and the feed rollers wiped firmly three times over their paper-contacting surfaces with a clean dry rag cloth moistened with rubbing alcohol.
If the checks are crumpled or otherwise damaged, please tell me how, and where in the scanner, and I will advise you further. Thanks.