That's normal. You or the installer deletes them, you restart FSX, he compiles new ones and the folders are there again. But their contents then differ. That new stuff are your new shaders then.
As said, if those new shaders and the low settings didn't help, there's no holy grail left anymore. Maybe you can borrow a more powerful card from friend to check the influence there. The mentioned GTX460 or a HD6870 might help a lot.

FSX first of all is CPU limited, but those cloud thingies actually are more bound to the graphic card and her bandwith and overall GPU performance. I know that the advertising of your card might explain some game capabilities, but they are very, very limited there.
So if your CPU isn't too weak, maybe a card update helps.

Maybe you can install some lower resolution clouds or get rid of the HD ones (if e. g. REX has installed those at your system). This should help a bit.
I'd search the Avsim library or so or would use REX with a setting of low resolution clouds to test this.

If you reduce the overall texture resolution with the slider in FSX, you will also free up some space, but lose quite some image quality. You can test this though.
One notch below very high at 'Global Texture Resolution' or even one step further down does this. find that slider at the Graphics setting page in the FSX settings.