Hmm I think it COULD be your Mobo.. If the AGP bus on the mobo is 4x instead of 8x then your FPS is getting screwed..
I had a similar problem with my Geforce 6800 AGP 8x\4x but as soon as I upgraded my mobo to a AGP 8x one my FPS on HL2 Shot up like a rocket!!! I used to get 40-50 fps tops (Average 28.4) but now I get 110-120 fps tops (Avg. 84.3). Every other component on my RIG was the same the only change was the mobo and the AGP bus.. And the funny thing is Battlefield 2 started running smooth as silk right after the upgrade.
I run my games at 1024x768, 2X AA, 4X AF, Med-High details.
SPECS:
ECS AGP 8x Mobo
Athlon 64 3200+
BFG Geforce 6800 OC AGP 8x
2x 512 sticks of ram (1 GIG RAM)
Creative X-fi Extreme Music sound card (SWEET 7.1 SS audio)
550W PSU
250 GB Hitachi Hard drive Deskstar (7,200 RPM)
Black case with blue led fans all over the place..