Before I get to the solution, I'll explain a bit first about what's going on. Many media playing programs (including Windows Media Player, RealPlayer, QuickTime) and TV Tuner programs use a feature of the video card known as "hardware overlay." The video window is painted a solid color in Windows (usually a very dark red) and the video card driver/hardware "overlay" the video image over that solid color. So the result is, you see a video image, but as far as Windows screen capturing is concerned, it's just a window with a solid color, just as Windows made it.
Only one program can use the video overlay at a time. This is what makes it easy to get around this problem. First, make sure all your media-playing programs are closed. If you have a TV Tuner in your computer, start the TV program. This is the easiest way to make sure the video overlay is already occupied. If you don't, open Windows Media Player, start playing a video file, then pause (not stop) it. Now, when you open your QuickTime movie, because the video overlay is already in use, it will have to draw in software directly onto the window. This will allow you to capture the video image using any normal means.
If this doesn't work, go to "Control Panel" -> "QuickTime" and choose "Video Settings" in the drop box. Click the "Safe Mode (GDI Only)" option, and click OK. This will disable all hardware acceleration for QuickTime video playback and force software-only drawing. You shouldn't use this method unless you have to, though, because this method will significantly reduce your QuickTime playback performance.
Hope this helps!