Nice theory, but unfortunately incompletely. To maintain backward compatibility with the previous decade-and-change worth of documents, GUI apps in OS X (e.g. TextEdit) generally use the Mac line-ending convention (CR), while BSD-derived command-line programs (e.g. perl) use the Unix one (LF). This could be charitably described as a mess.

I agree with your solution, though—make FTP work right, and the problem should go away. There might be a more specific solution to this specific problem as well, but absent more details on the nature of the program, it's going to be tough to say anything very helpful.