SOLVED!
I feel like an idiot, but solved my problem simply by reseating my card. Can't believe I didn't try it before, but I suppose the fact that it worked so well in some games just threw me. Complete answer is copied below, Link Removed due to 404 Error:
Well, I've solved it! Unfortunately it was the last thing I tried (edit: thinking about it, this is sort of inevitable as I didn't need to try anything else afterwards, but you know what I mean).
Noticed that GPU-Z was indicating "PCI-E x16 @ x2". Ignored it before, thinking it was something that I just didn't quite understand. Thanks to Google, I worked out to reseat my card and it popped up to "@ x16". Now running MW2 at around 40FPS with my settings (depending massively...