When I look at the original input file ... those are carriage returns at the ends of the lines.

Is it literally true that you are seeing "carriage return" (ASCII 0x0d) characters at the ends of your lines? If so, that may be a big part of your problem. On what sort of system do the files originate? Windows? On what sort of system are you processing the files? *nix? Line-ending delimiters are different on these two systems (and on others).