Looking at that picture, I can see that the intake on the right-hand side of the picture has no paint on it, the hardpoint cover has no paint on it and, unless I'm mistaken, it looks like the panel under the canopy has no paint on it either... and the rear section of the canopy, itself, seems to be having some issues too.
Have you tried applyng a different paint-job - even the stock one - to see if it also has similar problems?
If my PC started doing stuff like that with textures, my first thought would be that the gfx card was overheating and/or was on it's way out, I'm afraid.