[Anand Joshi]

According to the following link, it should not matter, but it also says the following.

http://www.mathworks.com/help/compiler/install-the-matlab-runtime-and-matlab-on-the-same-machine.html

Windows
To run deployed MATLAB code against MATLAB Runtime install, mcr_root\ver\runtime\win32|win64 must appear on your system path before matlabroot\runtime\win32|win64.
If mcr_root\ver\runtime\arch appears first on the compiled application path, the application uses the files in the MATLAB Runtime install area.
If matlabroot\runtime\arch appears first on the compiled application path, the application uses the files in the MATLAB installation area.

It is worth trying to set environment PATH variable such that MCR appears before Matlab.