I don't have a definite answer for the immediate issue, but a suggestion for the future to avoid this. Print the boarding pass(es) to a PDF file (there are many free options, CutePDF and PDFCreator are my favorites on Windows) then print a paper copy from Adobe Reader or whatever you view PDFs with. This has two advantages: you can save the boarding pass for later in case you don't get credit for the flights and you can reprint any time so long as you retain the file.