FWIW - I doubt the slowdown's related to anything but the CPU activity (could be wrong of course).

I've noticed the problem also. I don't believe it related to the CPU. It's related to the Manager updating its screen.

Screen updates on Windows are a critical section. If you're running a cpu intensitive program (normal priority, not boinc) and the screen saver kicks in, the screen will be frozen until it draws its first image. Most programs use double buffers so its not normally noticeable. I use the webshots screensaver and it's very noticeable.

If you minimize the manager, the video plays much better.