I came across your problem when I was trying to solve my own. Now I got back to you since I've managed to solve it.
First of all it appears that the MWMCR is only compatible up to .net framework 3.5.
Second make sure that you are generating the *.ctf file when building your function in MATLAB. you need to untick the option where it says that the .ctf is embedded in the application. Its in the settings of the deploytool itself.
Third when after you create the fill debug the program until you reach the code part in the static constructor of your classwhere it finds the assembly location and take note of the folder location.
string ctfFilePath= assembly.Location;
You would need to manually copy and paste the *.ctf file to that location and it should work.