No expert, but maybe your video card is too slow to keep up with the 3D effect at your chosen settings. Stranglehold was a straight unambitious console port which looked fine but I don't remember it having particularly ambitious graphics, whereas those other two could be maxed out with all sorts of screen bling. Anyway... just a thought.
CS - many thanks for response. I solved my own query about a week after posting, and it was all down to my own stupidity ! I had assumed the kit worked like a peripheral: once set up, no need to really do anything more, therefore I never thought of updating the drivers for the glasses. Once done, MW2 worked fine (though with me dipping into it every so often, I actually only completed it over Xmas !). Might go back and try Bioshock 2 again, as that was probably the reason that didn't work.
Certainly hasn't put me off the kit - I don't think I've come across such a cheap bit of kit, that adds so much more to the gaming experience.