Using skype 0.90.0.14 on Debian sarge under the ion2 WM, all the Skype windows except for the taskbar icon (which is in a window called "skype") are called "???". All my other windows (Emacs, xterm &c.) have sensible names; I think this problem might arise because ion doesn't have proper title bars, but something more like a taskbar window list, so it is using the icon text for the window names, not the window title.
Perhaps Skype is not setting icon text for its main window and chat windows?