This seems to be a common problem with 3D in some games that render shadows a certain way, as it also occurs with Nvidia 3D Vision. It is annoying and apparently avoidable.
This guy knows how to fix the problem, since his fixes for 3D Vision preserve shadows but correct their placement, including for Alien Isolation
http://helixmod.blogspot.com/
http://helixmod.blogspot.com/2014/10/alien-isolation-dx11.html
Water reflections are I think still incorrect.
In any case, maybe someone from Vorpx can collaborate with Helix to find solutions to these problems for Rift