Coverity recently published an insider's view to building a static analysis tool. It does a great job of explaining the practical issues in building a world-class tool that is depended upon by so many software development organizations in so many different industries.
If you've ever used Coverity, or any other static analysis tool, you will have a more healthy appreciation of how difficult static analysis can be. It just might explain some headscratchers you may be experiencing. Static analysis can never be perfect, but it can be darn good enough to provide significant value in the software development process.