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It may be that you are scanning using a photocopier. You might have lots of white dots in the scanned image (happens in 80 percent of copiers). We recommend not using a photocopier to scan images. - http://www.formreturn.com/support/scanners - One thing you can try is to scan it as a color jpg file at 400 dpi on the copier and see if it works.
can also happen in this scenario:
goes to print out and the bottom barcode goes past the print margin of letter size paper because it isn't a4.
Can also happen on some bubblejet printers where the print margin is too short at the bottom.