When Rumplestiltskin is in control, he is very aware of Neal's presence in his head, but when Neal takes over their shared body, Neal has no idea his father is alive, or even that they are sharing a body. It's almost like when Neal takes over, Rumple completely fades from existance. Neal had no idea he was there. What The Hell?
Well both of them were robbed of their memories. In Storybrooke, I highly doubt Rumple was aware of Neal, he probably just thought he was hearing things. But Neal clearly showed that he was aware of Rumple during A Curious Thing.