I just figured this out and had to share! I couldn't figure it out either, since I downloaded the entire plugin of YAPB and it worked. Now why wouldn't any other plugin work the same way?
Don't upload the entire file, or it won't work. Take each file from your plugin and upload via your cpanel or FTP. You don't need to upload the readme txt file. I just got Stats and Subscribe plugins to comments to work by doing this. And believe me, I have sat here for a few hours trying to figure out if it's a problem with the WinZip program, or possibly something else. So no, you're NOT stupid everyone!
I don't know how to upload batches of files. But if I figure it out, I'll let you know. Or maybe one of the nice WP people will let us know. E