If you're setting STDOUT to binmode, and your input file uses CR line terminators, then the output text is supposed to print over itself. A CR doesn't give you a line feed, it just returns the carriage to the left margin. You'll have to add a LF if you want to advance the carriage.

Of course, if your output is consumed by a program expecting CR delimited lines, then just ignore the fact that your lines overprint....

...roboticus