I had similar issues in the past with some video files I...aquired...
I came to the conclusion that there is no way in either WMP or Media Center to pick just one audio stream. I ended up using a couple pieces of software to pull the audio track I didn't want out of the file.
Rig1: System Specs.
Rig2: A8-5600K@4.4GHz / AsRock FM2A75 Pro4 / 8GB Corsair DDR3-1600 9-9-9-24 / HD7560D / Samsung DVD-Burner / 1.5TB WD Green + 3x3TB WD RED in RAID5
Rig3: Athlon X2 4200+ / M4A79 Deluxe / 4GB G.Skill Pi DDR2-800 4-4-4-12 / GT430 / Sony DVD-Burner / 500GB WD
Rig4: Phenom II x6 1605T @ 3.6GHz / Asus M5A99X Evo / 8GB PNY DDR3-1600 9-9-9 / GTX470 & GTX470 / Samsung DVD-Burner / 1.5TB Seagate