I get the file not found error when uploading some themes in zip format, but not others.
On the ones that have the problem, I notice that the folders are not created, but rather the files are named with the folder name in it.
so the file name in the root theme folder is actually
folder\sytle.css
somehow the back slash got incorporated into the file name.
weird…will look more closely at zips that upload properly vs ones that don’t tonight.