This is most likely the case.
I had a folder which had a .htaccess file that was hiding from view. It wouldn't allow me to delete the folder at all. Even recursive delete didn't work for me.
This did work for me. In my FTP client (LeechFTP, great little thing) I added '-a' to the LIST command (in the options menu). The next time I connected and entered into the directory, sure enough, there was the .htaccess file sitting there for me to blast away.
All's well now! Hope this helps ya!