You would get that when you use ss() if you attempted to use Rapid Acceleration mode or tried to generate code for a target.
The MATLAB Function block is primarily for blocks of code that can have code generated in order to run more quickly. If you are using a MATLAB Function block because you just want to call into MATLAB routines, then the Interpreted MATLAB block would be more appropriate.
If you do need Rapid Acceleration mode or need to generate code for a target, you will need to change the way you control the device in your release.
Note that current versions of the Model Predictive Control toolbox appear to allow ss to be used for code generation; see http://www.mathworks.com/help/mpc/ug/code-generation-with-simulink-coder.html