After much testing at various settings, I figured out what the issue was I posted a while back about my torso VATS percentages being so low (lower than head) even when I had a clear shot to wide open torso. For some reason, whenever I get the lag freeze when entering VATS I'm sure most of you are familiar with, the torso hit chance gets cut in half. I know that sounds bizarre, but I have tested it A LOT with a totally clean install no mods or anything. To avoid this lag spike I have to turn the settings WAY WAY down (not only AA off but very low resolution, low textures etc) to almost bare minimum, even though my FPS in the regular game world is fine on high settings. I also discovered that Sniper is working for me, however Commando and Gunslinger are having no effect still. Have they mentioned anything about fixing the VATS lag and/or Gunslinger/Commando? I'm very sure I'm not the only ones having these issues.

For some reason my VATS problems seem to have disappeared lately.

However I'm religiously saving every so often, and had a major fiddle with my nVidia card settings for the game, that seems to have fixed a lot of the stuttering and frame rate drops.