Using the Vegas Pro 15 Sony AVC/MVC Blu-ray template fixed the problem. I am not sure why the Magix AVC Blu-ray template appears to lacks the ability to embed Marker information, but now that I know I will avoid it when authoring to Blu-ray.
As a point of reference, the Magix AVC Blu-ray render template lacks the “Save Project markers in render Media File” option, while the Sony AVC/MVC Blu-ray template has this option.
–Rob