I think the issue here is the difference between DACs, which are 'dumb' devices, and an AVR or a Sound Card.
With a 'dumb' device like a DAC, each channel has a fixed assignment, typically:
1 - Left
2 - Right
3 - Center
4 - LFE
5 - Side Left
6 - Side Right
7 - Rear Left
8 - Rear Right
So if you send them a four channel source, they map the Rear Left/Rear Right channels to Center / LFE (channels 3 & 4).
When you send a Sound Card or AVR a four channel source, they know that it's a quadrophonic track, and map the Rear Left/Rear Right to the correct output channels (7 & 8).
I'm not sure that there is anything for Media Center to do here, because Media Center is behaving correctly.
When you play a four channel source and tell it to use the "source number of channels", it outputs a four channel signal mapped to channels 1-4.
If you set the output to "5.1 channels" it maps the output to channels 1,2,5,6 and if you set the output to "7.1 channels" it maps them to 1,2,7,8 ensuring that the sound is played to the Rear channels rather than the Center/LFE channels.
(apparently Rear Left/Rear Right move from channels 5 & 6 in 5.1 to 7 & 8 in a 7.1 signal, unless Media Center is doing the wrong thing here)
Jim - that would be fine by me, and it might help current and future users avoid the Source Number of Channels trap. Unless someone has a lot of 6.0 BDs or other formats - DVD maybe, but I doubt it - it should not cause a major problem.
The fact that 6.0 media exists means that it would be a problem if you tried to map all 6 channel sources to a 5.1 output.