in reply to FTPing
It is my understanding that it has to do with line endings in your script. If you send as binary, the line endings stay the same, no matter what the OS is on either end. This will, of course, cause problems when you FTP from something like Windows or Mac to Unix (or any other combination of differing OSs).
If I recall correctly the ASCII mode automagically translates the line endings in your script to the kind that the destination OS uses.