My guess is that your local file has, for example, only CR characters as end of line markers, and you upload (FTP) in text mode... Whoops, all the CR characters are gone. Are you by any chance using a Mac on either side of the connection?
Anyway, if that's the cause, think about uploading in binary mode, which may require an extra conversion on one side of the transmission, and for which you may even use a perl script to fix it. Either that, or you make your parsing script more flexible, so it accepts any conventional line endings (CR only, LF only, CR+LF).
Your file, as you have shown here, is kaput. Upload it again, more carefully this time.
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