Think the two months between flights makes most sense. Amy was a ganger in the first scene. Not everything's got to be twisty-turny plotty-wotty (although it's brilliant when it is).
There's one idea that I do quite like, that says she could've been switched mid-picnic. We see the Silence are there, but they don't really do anything. I don't think the Silence took her, though. And I don't think they're on the side of Madame Kovarian et al., to be honest. Jimmy Bighands in the toilet tells Amy to tell the Doctor what he must know, and what he must never know. Presumably (although "presumably" is a dangerous word given that Moffat is a tricksy little hobbit), what he must know is the pregnancy, and what he mustn't know is his own death. It worked, Amy eventually told him about both of them. But the thing is, it was helpful information. The Doctor might've never rescued Amy if the Silence had never got her to tip him off.
Which does leave the mystery of what their beef was with Melody Pond, and why Steve Silent et al were so eager to get her into a spacesuit.