Win32 == binmode your binary file handles, perl does on the fly conversion between \r\n CRLF and \n on Win32 which is probably the issue. You may have to binmode STDIN and STDOUT as well.

binmode THEFILE; # :-)
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BTW you have heard of die it will print an error message for you and exit with a true value like for example 1 so do{print "Could not close $file: $!\n"; exit 1}; is what most people would write as just die "Blah $!\n"