Interestingly, I just tried this same 720p .mkv file on my other P4 2.4 Windows 2000 computer. It's graphics card is a Radeon 9800 Pro, a few years older and considered a slower card than the Geforce 8400gs(PCI card). But the Radeon 9800 Pro is an AGP card, and the .mkv file ran almost perfectly on this computer. So it looks like the difference was the PCI vs AGP, and AGP trumped everything else.
My other lonely, broken, holy crapped, loooong past its date, Windows 2000 P4 2.4 worked pretty well with the older(2003) AGP card. As it has with everything else I run on it (including the Firefox 21, Adobe Flash 11x). It is tricked a bit with an Extended Kernel and various Unofficial Updates Rollups from blackwingcat and Tomasz and an Application Compatibility Launcher. Personally, I prefer older versions of most programs, so if I can watch the occasional HD soccer game or movie, then what may be the stablest(and least annoying) Windows OS is good enough for me.