Just to maybe explain what was actually going on a bit better... this is what's in the download package:
In your file system, you'd have had this:
Obviously there'd be all the other files too but to keep it simple we'll stick with these two. If you were to copy all of the download package over, what you would normally end up with is this:
I.e. it now has the file that was already there (config.php) and the file that was in the download package but wasn't already uploaded (config.default.php)
But what you got was this:
Because it effectively erased what was already there and just uploaded the new files.
Similarly, the uploads folder in the download package would look like this:
In your file system, you'd have this:
Again, what you'd normally expect to happen is to stay on exactly what you had before, because nothing's changed, and the folders you're uploading, although empty, already exist on the server. However, it ended up with just the empty folders because again, it erased what was already there and just uploaded the empty folders in their place.
The same problem happens with Finder on OS X and it's the thing I hate most about using a Mac. It's very counter intuitive. Hopefully that explains what it was doing though and hopefully I haven't just confused you