If it's anything like Sony Vegas Pro 10 then the Blu-Ray 1440x1080-50i 25Mbps template is called Blu-Ray 1440x1080-50i 25Mbps template video stream. That's the clue. It's rendering the video only. This enables you to render trhe audio separately in whatever format you like, then assemble them in DVD Architect.
I don't know if you can do this in MSP, but in Pro, when you chose the rendering template there's a "Custom" button. Click that, go to the audio tab and check the "include audio" box.