My theory is that there are two versions of the same timeline that we're dealing with here.

The first is the original version of what happened, which is not the version we're seeing. The version we're seeing is what's happening after the future Doctor has gone back and started tweaking things in his own timeline, being very careful not to let his past self know he's doing it.

Future Doctor has been altering the timeline of the entire season as it has progressed. I'm not sure how his interference would have caused Present Doctor to trace the crack differently the second time through, but it might explain it.

I think Future Doctor was there at Amy's house right from the beginning (the dark shape moving in front of the camera). I believe he intentionally started the TARDIS phasing that caused Present Doctor to run out of the house and leave Amy behind. It's possible he also sabotaged the TARDIS so that it would arrive 12 years later. In the original timeline, it all happened differently than what we've seen, but it ended badly, so badly that the Doctor is going back in his own timeline to push things in a better direction, a direction where Present Doctor has a chance of figuring it out and saving the day before it's too late.

There are two ways Future Doctor could be doing this. One, if the TARDIS is destroyed, he could use the cracks to move about, since they always seem to show up around Amy. Two, if he still has access to the TARDIS, we've seen that it can be made to fly and land silently if the brakes are taken off (as River Song demonstrated). He could appear without alerting Present Doctor.

I also believe that Future Doctor appeared before seven-year-old Amy after he made Present Doctor leave. I believe he put the brakes on and made the TARDIS (future TARDIS) appear before her, which explains the shot near the end of Eleventh Hour where young Amy hears the sound and looks up. Future Doctor told her something -- "remember what I told you when you were seven" -- and then left again, possibly telling her (again) that he would be right back, knowing that Present Doctor wouldn't arrive for 12 years.

I think this could also explain why the Present Doctor is having such a hard time focusing, and keeps missing things. His own timeline has been altered (by a future version of himself), putting his mind out of sorts somehow (maybe he can feel that something is wrong, but doesn't know what).

This could also, potentially, explain how other beings (Prisoner Zero, the angels) know what the cracks are, and Present Doctor doesn't. Both of them are, in some ways, time-related beings. Prisoner Zero travelled through time with the crack, while the angels feed on time energy. They can perceive things in the way the Doctor normally can. The Doctor, however, has had his own timeline tampered with and cannot properly perceive the things within it that have changed, because it's a matter of perspective, and this time the perspective that's changed is his, not someone else's.

In a nutshell, once upon a time the universe ended because of something Amy Pond did. The Doctor wasn't able to stop her, or perhaps he never saw it coming. Cracks began to spread throughout reality, devouring all of time and creation. They could not be contained, and could not be stopped.

The Doctor realized that the only way to stop the cracks was to go back in time and prevent the explosion, but he couldn't directly interfere with his own actions in the past. He had to trust the mission of saving the universe to the only person who might be able to figure it out in time -- the past version of himself. So the Doctor travelled back to the start of things, and began altering the timeline, sewing the seeds that might help his past version figure things out on time, if only he could be smart enough, clever enough -- "I don't know, I'm still working it out" -- to decipher the clues and sort out Amy Pond in time. The new timeline that the Doctor created for himself is completely designed to put him in the right situation where he has a chance to figure Amy out and stop whatever she'll do in time.

I believe this season is the story of two Doctors. The one we can see, struggling through an altered timeline, unknowingly acting as the universe's last hope as the end approaches; and the one we can't see, operating in the background, trying to give himself a second chance to save the day.

... if all of this turns out to be right, I'm making myself king for the day.