I've had no problems connecting to and working with files located on a Windows server until the latest update for Cyberduck. Now, the permissions are incorrectly displayed and I can't change them. When I double-check from a Windows box, they are correctly displayed.
Too bad for Cyberduck. I liked it. I'll be forced to work from my crappy Windows box until I find a replacement FTP client, or Cyberduck gets another update with a fix.