Ok, so that’s an FTP function not using software from your own computer, but more like an upload function in your control panel or something? I don’t have experience with that.
Can you compare the files on your computer with the files on the server? Like, opening the style.css with notepad from your computer (for example) and view the file itself on the server? It’s a long shot, but perhaps something just goes wrong in the transferring process.
Did you try another method to copy the files to the server ((another) FTP program or something)?
WP itself, did you upload it yourself, was it already on the server or can you use some kind of automatic installation?
Just wondering, did you try to add plugins and does that work? Maybe another option can be the One Click Plugin Updater also allows you to install a theme. Just as another option to try if another method works better.
Questions, questions.