The issue is when you shift the viewpoint for the eyes, you simple don't have some of the pixels to render, so you have to fill the holes with something, it can look passable, but to me at least the artifacts are very visible.
The only right way to do it is render twice, and have no shaders that either don't write constant Z or assume they are in screen space.
There are almost no PC games that are artifact free with 3DVision, it renders the frame twice, but the patches don't usually resolve the shader issues.
Having said that with patches games like Skyrim look spectacular in 3D, with only a couple of remaining issues.
Uncharted 3 on PS3 was about the best example of how good it can look, since the dev actually spent time on the 3D version, rather than trying to retrofit it in the driver.