Ah - sorry, I didn't read your first post properly. I think I now see what you mean.
When you go to:
Site > manage sites > (select your site) > Edit > Remote info:
Have you set the 'Host directory' to the proper setting? The Host directory setting should have been provided by your hosting provider with your login and FTP details, see attached pic for example of mine.
What have you got for yours? I suspect it should be something like 'wwwroot/' or /wwwroot/yoursite.com/ or somesuch.
I think the correct setting here would solve your problem.