Fix minor scons sphinx warnings

The changes here fix some warnings in the build process for the MATLAB interface that I introduced with my documentation changes. I also tried to fix some of the warnings in the Sphinx documentation, but several of them I could not fix. These I noted in the `.pyx` files. I'm not sure if the changes to the Sphinx stuff are worth the churn/comments (the MATLAB stuff I think should be fixed). Any thoughts?

Thanks!
Bryan