Line ending in Win32 is "\r\n", so you probably shouldn't strip the "\r" chomping the input line, as per sh1tn suggestion or, golfing a bit:

open INFILE,  $ARGV[0] or die $!;
open OUTFILE, $ARGV[1] or die $!;
local $\ = "\n";  # Appended to any print invocation
print OUTFILE while(<INFILE>);
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