A couple of things: first (and not your problem), the argument to 'use lib' doesn't need either backslashes or a trailing slash.

Second, if you're using the "same file" in both, it may be a difference between the Unix and DOS line endings in text files -- Unix uses a single \x0A character and NT uses \x0D\x0A. But both appear as "\n" to Perl in a text file ON THE APPROPRIATE SYSTEM. However, you could have problems with line endings being different. You could try changing the line endings on the Unix system where it'll be easier to do using recode or a Perl one-liner:

   perl -p -e 'chomp; print "$_\r\n"'
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or in place:

   perl -pi.bak -e 'chomp; print "$_\r\n"'
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