You cannot have both MATLAB and MCR installed on the same machine and consistently run at deployed app.
I have not had any luck if both x32 and x64 MCR are installed, but you can have different version of the MCR installed, although that's not optimum.
If you have an x64 MCR deployed MATLAB, you must use x64 in your c# app.
This is not clearly documented, and these are from my experience deployed the same MATLAB base as a COM DLL, an x32 .NET assembly, and an x64 C++ shared library.