PK brought up a good point in this thread about Neo waking up in the Mobile Ave train station.
What if it wasn't an accident? What if his counciousness was unceremoniously 'booted' there when he tried to reach the Source in the Real?
I'm thinking this way since the train station is obviously beyond the Matrix, and is also somehow connected to the Machine Mainframe (where all there programs are stored).
Further down this line of reasoning, wouldn't said conciousness manifest itself in the simulation as an RSI? Could that have been the reason that Link couldn't see him?