I hadn't really noticed that my mplayer-video-thumbnailer had not been working properly in under Gnome3. Some thumbnails were getting updated and others were not. So I finally tracked down the problem and was able to solve it in about 20 mins. It turned out that nautilus had changed its configuration for thumbnails from a gconf entry to something similar to how Thunar does it.
So I made some changed and bumped the version
You can download it from here: