When using SharePoint Designer to open a site directly from it's directory (like E:\site\ ) via the "Open Site" button, it is possible to receive the above error.
We experienced this issue with one directory, while all the others worked just fine. The strange part was that I was able to open the subdirectories of the failing directory. With this in mind, I made a new directory and began copying separate files to the new folder. After a few files, I tried to open it with SharePoint Designer and this was always succesfull. When I copied one of the last folders - which was a hidden folder - I got the error again! From that moment I knew what the cause of the problem was.
It was the hidden folder "_vti_pvt". I don't know what exactly is going wrong, but after deleting the folder everything went like it should. Watch out however! In my case the folder was empty, but this is not always the case. Do not delete the folder if files are located in it!