Not sure if this weill help, but I'm using Mac OS X, which is UNIX behind a pretty GUI interface. I download directly to the server, and unzip, using Stuffit, and place files directly. No FTP stuff. Which, depending upon how you write things, may have something to do with line breaks and the like.
However, I've installed tons of programs and hacks, without any problems, without FTP. And, it all works great.
let me know what I can do to help. The quote thing is a popular part of my site.
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