I obtained it with my 3DS, not sure about the person I'm trading with though. Are you suggesting that our DS systems are unable to communicate due to obtaining the FC on a different DS model?
EDIT: Massive misunderstanding! haha, the individual I'm trading with was adding my FC on the '3DS friend code menu' not in the Pokemon game, he was giving me his 3DS FC hence why it wasn't registering... Thanks for the quick reply regardless! ;D