Only addressing the "glitches", or flashing in brightness for particle effects (which smokes are)... This description would suggest you have Effects=2 in your conf.ini. If so, try Effects=1. On the "2" setting the game applies lighting calculations to add shadowing to the particles (each texture for a smoke effect, for example). This shading makes the Sun-facing side brighter and the opposite darker. When the particle count gets high, the graphics engine glitches, with the texture flashing you describe. Moreover, with Effects=2 the greater consumption of CPU cycles lowers the frame rate.
Setting Effects=1 bypasses the shadowing, which might not be so 'pretty' for some folk. But at least the schizophrenic flickering between light and dark is avoided, and fps is higher. Smoke particles using textures having a variation in tone and color (subtle) can overcome the lack of shadowing. Indeed, I mostly prefer this look with Effects=1, because the added shadowing with Effects=2 tends to be a bit too exaggerated, making the smoke puffs look too 'solid', or substantial.
Now, Effects=1 is not the complete savior. When lots of particles are being drawn, some may briefly disappear. But at least there is none of this bright/dark flashing.