Just reading the Doc Who article in the Radio Times, and River is in episode 7 'A good man goes to war', its the episode where she reveals who she is to the Doctor. Also, the bio for that episode says that the the Doctor and the lone centurion (Rory) are racing across the Universe to save the women they love....so I take it that means Amy gets separated from the Doc and Rory at some point in the earlier episodes.