It sounds to me like you are possibly uploading to the wrong location.
Check your site definition. Make sure your server root folder IS NOT in your local site folder.
If it is, you are going to accidentally be uploading to a redundant root folder on your server. The server root should only appear in the FTP information, not in your local file info.
If you could post a screen shot of your expanded Files window here, while connected to your server, it would determine pretty quickly if that is the issue.