Does the internal battery work? If you play it and it says the internal battery has run out then time based events (including berry growing) won't happen. That's what's wrong with my Pokemon Ruby.
On Emerald the internal battery never works because since they are all made in china when they ship it the police check the memory inside to make sure no one put secret messages. It only affects emerald, ruby, and sapphire however. But, all you need to do is be careful with the game and nothing will happen.