The all files in subfolders shows in root folder

Connecting to server, and I see a big list of files, that are really placed in subfolders, not in root folder. Look here, a little example
Real structure:
The SmartFtp shows that in httpdocs:
And when the structure of site is rather big and difficult, you can imagine what kind of problems i have with it (the files of subdirectories are showed in root directories)
When I'm trying to delete file or directory, who really "not here", smartftp gives me error 550 "No such file or directory"

Sorry for english, may be some mistakes)