Have you registered at www.onecnc.net yet? There is a forum there where the masters participate, and might shed some light on your advanced problem.
I would be glad to discuss the issue on cnczone, except I don't have any answers for you.
I suspect that you might not be using the optimum method of creating your surfaces. Even though they look okay, and surface okay, there can still be problems due to some technical detail of your construction methods, or the type of surface you chose to create.
This is fresh on my mind lately, so pardon me if I have insulted your modelling skills . I personally have blundered my way through several models and thought I was getting a grasp on things, but I have discovered that I have a lot to learn yet.