In the settings for the remote server, make sure that the WebURL setting is the Correct URL address to open your site. It should be the http address to access your site, the address you should use in a web browser to see pages on your site.
If the FTP Connection does not default to the root of your webspace, make sure that you enter the root directory. For example, some hosts have the FTP settings connect under the web space, when you connect via FTP you may see a public_html folder or an htdocs folder that is the web root. if that is the case, you need to enter that for the root directory.