So i know a couple of fixes:
1) Download Nvidia - ATI Fix, this fix is for the shaders, becuase the game was designe for older videocards, thats why this might help you, so google "metal gear solid 2 nvidia ati fix"
2) change the compatiblity -> right click on both mgs2 and mgs2_sse -> properties -> compatiblity ->windows98.
3) If the problems persist, try patching the game to 2.0v(this will change both mgs2.exe so you might want to keep the nvidia ati fix after doing this so you can re-paste.