I have very similar experiences with Prey. Because the game runs so smooth & when walking upside down for me, it really messes with my head, like in a way to make me vomit. On some occasions, especially, walking for minutes at a time upside down makes me quite queezy.
I also had problems with Half-Life 2, like with the motion sickness (especially the airboat chapter). So this does effect me quite a bit. I'm not sure though if Valve patched it through thier updates though...