I don’t have any experience building Simulink models for real-time simulation. I have read some comments about it in the MATLAB/Simulink documentation that I sent you. I do not think you have to modify the header file; I think you need to make sure MATLAB is setting the appropriate preprocessor flags so it uses the correct header files.
My concern is that your error message seems to indicate that Matlab is finding duplicate header files, some of which are in the real-time-workshop toolbox. The paths to the included headers are set by MATLAB.
I would recommend that you read the MATLAB documentation on the C template for level-2 S-functions and see if perhaps the API for MATLAB 2012 is different than what is implemented in FAST. Or, perhaps there is something else that needs to be set when you run it for DSpace.