All of the sudden, every selection I make is the inverse of what the shape is, which makes it very annoying to render since inversing the inverse does not make the original shape, and therefore you get ugly halos and such. If anyone knows how to fix this, I'd be most appreciative.
ive never heard of anything like this happening. re-installing is always a good thing to try like sapphire said.
show a screenshot of your settings while in pen tool and probably it will help ppl out as to how to solve your problem.