I asked a related question a while ago, and got many helpful replies that are also applicable to your question. Please see Newlines: reading files that were created on other platforms.

In short, I chose to preprocess the input file to convert all newline characters to the current system's newline character:

    $file =~ s[(\015)?\012(?!\015)][\n]g;
    $file =~ s[(\012)?\015(?!\012)][\n]g;
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HTH