The problem here actually isn't Media Center, its an unfortunate thing which people tend to do when encoding videos (including some cable networks). When we talk about aspect ratio we're talking about the aspect ratio of the video picture. Now what you have is people encoding black bars into programs so that the aspect ratio in 4.3 will correctly display the full 16x9 picture for instance, with black bars on of course though. Some TV's and devices can make attempts to try and fix this by detecting the black bars and removing them.
In most cases though your going to find you have trouble with any video which is broadcasting a video with blackbars actually in the video. Its really hard to try and explain this clearly I hope this makes sense.
I'll give you an example of when zoom won't work. For instance I recorded Family Guy which was broadcasted in 4:3 over a digital channel. However it really wasn't broadcast in 4:3 at all. It looks like it, it has big black bars at each side. It looks correct on a normal 4:3 tube TV, and on my widescreen 16:9 it has black bars. There-fore you would assume its 4:3. It actually isn't, its been broadcast in 16:9 with the black bars as part of the actual picture. the 4:3 tv doesn't care as it simply cuts it off, the widescreen however shows it, you can't zoom it or stretch it because it already thinks its the right format!
You can actually see clues of this on some channels as channel providers have started putting their network logo in the black bars outside of the main picture.