the file headers get malformed when they are ftp'd incorrectly...and produce wildly inconsistent results...page works once, and never works again etc.
Why? I believe that simplisticly it has to do with how the line breaks in the files are written...binary preserves them in a way that leaves them functional, ascii replaces them with 'place holders' that cause errors...
good example to see it in action...check out the backpack module. Does a great job saving and importing your MySQL data from xoops...BUT save the data with back pack and try re-inserting it with phpMyAdmin, and it throws errors all day long.
Another easy way to graphically see what I am referring to is to open a php file with notepad, and open an exact duplicate of the file in wordpad...the difference you see there, means a lot to the server.
Ipswitch WS-FTPPro is a good alternative to CuteFTP, which didn't work for me very well or consistently either