Did you not read the above, the Nv CP AA/AF settings have no effect on the game at all.
From the Stalker FAQ.
10) Why doesn't my anti-aliasing work?
A: S.T.A.L.K.E.R. uses a technique called "deferred rendering". Because of this, anti-aliasing has no effect on the game engine. (This is also used in Ghost Recon Advanced Warfighter and Rainbow Six.)
Therefore, enabling anti-aliasing in the driver control panel has no effect.
It don't work.
The rain glitches (if you mean the triangles), only happens when you go to the options menu, and back to the game.