You do not say which operating system you are running the Perl on. This is important because Windows has the notion of text files, whereas UNIX does not.

When Perl on Windows reads a text file it removes the "\r" for you, so if you are running the code on Windows, it probably doesn't have a "\r" in the record to remove! Perl then adds the "\r" (^M) on Windows when you write the file as text with a "\n" line ending.

If you wish to write a UNIX style file on Windows then set binmode on the file handle before writing the file.