I remember an interview where he said part of the problem is that he now doesn't WANT too moonwalk in that spot during billie jean. He's been doing it for 25 year and people EXPECT it, but he wants to just dance the way it feels... so who knows? Maybe we weren't going to see the moonwalk in its regular place.
To be perfectly honest: the billie jean segment is a BIT of a let down (probably shouldn't have been saved for near the end). The sync is off, which is troublesome. And while michael is still amazing he does say: "thats just a feel for it" which makes it clear that he's not going full out (and how AMAZING the real thing would have been).
it still SOUNDS amazing though.