I don't get why this is such a problem to fix. Wasn't 3d vision supposed to simply render the exact same frame from two slightly shifted angles instead of the one provided by the game engine?
If the projection of the menus is on a fixed (invisible) plain, it should be rendered correctly in both 2d and 3d mode.
You'd think, sadly 3D finally took off right as GPUs became really flexible. The fact that it can do any of this at all is actually pretty amazing - things like the viewpoint, direction, projection information etc don't go to the GPU via named slots anymore, all the driver gets to see is that you've given it a block of "data" and a shader that's going to do stuff with it.
To give another example, there's a lot of stuff gets drawn to a lot of textures during a frame. Suppose we draw some shadows from a light's perspective, it wouldn't make a lot of sense to draw them a second time with an offset eye position when doing the other eye, but it looks like a very similar job from the driver's perspective.
My guess is that they just take the final image, probably find the most recently-written depth buffer that's the same size and shape, and apply parallax to it. Since they don't know what "near" and "far" mean in real terms, they give you a depth-effect slider to let you tweak it until it looks right. It's not ideal, but it's very fast and general-purpose.
Native support is always going to be better, even if it takes the same shortcuts, because the game developers know what other limitations and shortcuts they're dealing with. They know if they're using a depth-range split, where it is and whether they've marked pixels on either side in some way. If they have to support transparency they can do the reprojection stuff first, maybe, then draw the transparency in full for both eyes. Or they can bite the bullet and do two full-eye renderings if they think they can afford it, and not accidentally end up redrawing the shadows and other offscreen junk for both.
Anyway, this is probably more interesting to me than it is to you, but hopefully you get the picture.