I presume the swap occurred during the second episode when Amy was captured by the Silence after telling the Doctor she was pregnant, and then they rescued an Amy who said it had been a false alarm. I suppose they'll have a go at explaining it next week - it would be extraordinary if Rory didn't raise objections after his experiences during the previous two episodes. Oh dear, I hope they're not going to mess Rory's characterisation up.

You're also right about Jen - why is she the most bloodthirsty of the Gangers when she's the one who's received most kindness from a human? The only thing I can think of is that she's displacing her guilt about killing Flesh!Buzzer earlier on, but if that was the idea I think they might have spelled it out.