Only the "active window was encoding; the other three were just sitting there, occasionally getting the odd update.

Yep. Windows has this concept of "foreground application priority boost". Go to Control Panel, System, Advanced, and under Performance, hit the "Settings" button. It allows you to tweak this value. On desktop Windows (2000 Pro, XP Home, XP Pro) it's set to boost the foreground application. On server Windows (2000 Server, 2003 Server) it's set to not boost it.

Personally, I'd leave it alone. All it does in the "server" setting is make the scheduler fairer. It still won't benefit you to run more encoders than you have CPUs.