Ah, yes. This has given me problems before, often with Unix-style programs operating on DOS-style data. Good to remember to check for these sorts of issues.
In the quest for a utility to convert between *nix and DOS newlines on a regular basis, I have found flip: Newline conversion between Unix, Macintosh and MS-DOS ASCII files to be useful. It not only converts between DOS and Unix file formats, but also includes a handy -t command-line switch to tell you which format a given file uses.
HTH,
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