chomp will remove only the newlines based on the current value of $\ which is the OUTPUT_RECORD_SEPARATOR (in English)

If the file was written on win32 (where $\ defaults to \n\r) and then uploaded to unix (where $\ defaults to \n), chomp only catches the \n and misses the \r.

So you can do this:

foreach ( @config_pairs ) {

    chomp;
    s/\r//;

    # more stuff
}
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Jasmine