Yep, I did, but I thought you just left the settings as they were, as you didn't mention whether turning them off solved your fps problem. Did it?
As for why they're on, I'm not sure. It could be a CS/HL issue (they detect your card and improperly enable those settings), or maybe you had CS installed before you installed your 9800, and it just kept those settings. In fact, I'm not even exactly sure of what those settings I listed do, so you should probably Google for more info if you want to know why they're set the way they are. I do know that upgrading to CS 1.3 from the previous version made performance tank with my Rage 128 on a P3-866 (it was slow enough already, but we're talking tanking into single-digits). I finally figured out CS somehow had those settings (TruForm) enabled on my decidedly non-TruForm card, and disabling them fixed the massive framerate dips with multiple ppl onscreen. So I'm leaning toward it being a CS issue, in that it improperly detects ATi cards, or unintelligently enables (or doesn't disable) certain settings. But CS is free, so I'm not really complaining.
Out of curiosity, have you tried playing the game with vsync disabled? It should boost your scores dramatically, though it might result in some "tearing" of the onscreen image. I'd try it out, and leave it off if you don't see any visual problems.