Where did you get 1.1.39? Did you install the package from here (http://www.winehq.org/download/deb), some other source, or compile it yourself? It sounds as if you manually installed the nVidia drivers instead of installing the packages from the Ubuntu repos. Any particular reason for that? I'm running Wine (compiled from Git) on a 64-bit Karmic and 64-bit Lucid machine with nVidia cards and the nVidia drivers from the Ubuntu repos, and have not seen the issue of which you speak.
