I understand all that... BUT... HL, UT, and AVP only required an 8 MB card... BF1942, etc etc etc recommend a 128.
That is why I think it is your video card...
1. Lower your resolution/quality of effects in the games where you lag.
2. Get a better video card
I have a friend who has an AMD 1.8 Ghz, with a 64 MB card, but it lags until you turn down the res to 1024x768 and lower the view distance and effects quality.
Try changing your video settings (in game) to medium for everything... see if your mouse is still laggy. If it is, then it is a mouse problem. If everything is fine, you just narrowed your problem.
DO NOT go by UT, HL and AVP... those are 4-5 year old games. Test with BF1942 or UT 2003.