I use frontpage and have no problems uploading files that begin with a dot.
So maybe you should try frontpage.
Actually, I'm not able to view, download, or upload any file or directory that begins with a dot. I've tried Dreamweaver for my basic uploads, but when that didn't work, I tried WS_FTP. I have it uploading in ASCII, but I'm thinking it's because I'm on a Windows OS and there would be no filename... just an extension. But I can't even manipulate the files unless I go through my hosts web client. Any ideas? I'm stumped.