If you e-file, your tax data is in an XML format (ask a computer-nerd friend) and is not a copy of your printed forms. Based on what you said, I would believe that the XML data packet for your return is correct; it's the print software that goofed up.
If you can see the numbers on the 5329 in Forms mode, I suggest you get the blank 5329 in your printed tax return, and manually enter the numbers for your own records.
Oh, and you should be able to file.
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