I'm not sure about Cute FTP, but I'm using FTP Pro. It has 3 buttons in the middle of the two directories, the bottom button is a toggle switch to change between, binary, ascii, or auto. When I'm uploading script it is important for me to make sure I toggle it to ascii, as it sometimes defaults to binary (yes, I have my defaults set for ascii on .txt, .cgi, .pm, etc).
Check your program "help" files, they may shed some light on this for you.
vik