I'm not familiar with Total Commander, so I don't know if it could have any impact on your inability to create folders in an .htaccess protected directory. I routinely create folders in password protected directories with other ftp clients, and the shell, without problems.
You mentioned that had webdav setup, but that you disabled it - could it be that the sustem has not fully disaled it yet? Possibly waitng a bit could help.
I suggest trying to create a domain via the shell, or another ftp client, and see if the problematic behaior persists.