You may have a problem with the point locations in the template that is causing the undesired results. I have alos found these types of results when a template transition has the first template including a feature that should be traingulated, and then the second template has the same feature (point name) but it is located in the subgrade.
Since a surface feature can only be one of two ways (triangulate, Do Not Triangulate), it will traingule down to the subgrade point.
Other than that, I may need to see your data to analyze and advise.
HTH
Thomas