Why use IO::File? Also when you read the input file, the line terminator is still there, and then you're adding another one with your join. Plus is your script running on Windows or Unix? If Unix, then the \r will be read, never gets removed, and then gets into the output.

I would handle this as follows:

open(my $in, "<", $inputfile) or die "Can't read '$inputfile': $!";
open(my $out, "<", $outputfile) or die "Can't read '$outputfile': $!";

binmode($out);
while (my $line = <$in>) {
  $line =~ s/\r\n?/\n/g;
  print $out $line;
}
close($in) or die "Can't close '$inputfile': $!";
close($out) or die "Can't close '$outputfile': $!";
[download]

This code should work on both Unix and Windows.

I actually leave out the closes usually. Putting them in will tell you if, for instance, you had a full disk. But I usually don't worry about that.