It goes up to Eleven!
Okay, first off let me say I am enamored and smitten and totally taken by Eleven and Amy. While I haven't actively hated any of the Doctors or their companions, this is by far my favorite.
Now. Onto speculations.
For my American friends, I hope this isn't a thing in the series, because BBCAmerica cut it out of their airing of episode 1. When the Doctor went back for Amy, 12 years after fish custard, 2 years after the Atraxi, the initial sounds of the TARDIS landing were shown to the clip of Amelia (young Amy) sleeping wherein she woke up, but it was Amy who went running out to meet the Doctor. Some have speculated that it was just a dream, and it very well could be. It was never explained.
However, the Doctor was noticeably different when he went back to Amy in episode 5 when she was sitting in the forest with her eyes closed. The first time he left, he had lost his jacket to the angels and was only in his shirt with both sleeves down. When he came back to tell her to trust him, he had one sleeve rolled up and his jacket on. Plus, he was so much more physically affectionate with Amy the second time, whereas the first time he left, he just patted her on the head and said "later".
I think it was a different timeline Doctor there, telling her what she needed to know, and he went to a time where he knew that Amy couldn't see him, if he was wearing different clothes.
Either that or the editing department cocked up and I'm reading way too much into things.
If people want to talk about it, there will most likely be spoilers in the comments. Just giving you fair warning :)
Eleven ♥_♥