I just had a thought.
The Doctor either knows that Amy's pregnant, or just knows that something's weird with her Schrodinger's Foetus. Ganger!Doctor presumably also knows this. Now, some of the Gangers have been shown to have quite different personalities than their counterparts (although this could just be due to the fact they were constantly killed and reborn, and can remember that, whereas Ganger!Doctor hasn't). So, what if Ganger!Doctor decides he doesn't want to keep it a secret from Amy?
Probably been brought up already, I guess XD