The trainman is his name. He's not a time keeper, he just wears the watches because its part of his character.
He is made to represent the ferryman from the old egyptian myths. In ancient times the ferryman would transport souls from the land of the living to the afterworld.
In the matrix, the trainman acts as a ferryman between the real world and the machine world. Limbo is not a loop. The fact that rama and family are being put on the train means they are being sent BACK into the matrix, OR, they are being escorted OUT of the matrix to the real world (into machine bodies, etc)
The ferryman aspect makes sense in terms of the limbo aspect. Its possible that this train is the metaphorical representation of something which occurs every single time a human jacks in or out. They take a train from point a to point b, but never realized they were making that journey because its almost instant.
However, if something where to go wrong with the link, or as in etm, the mind became fragmented or separated from its host, it makes sense that the conciousness would remain in between the two worlds. In limbo. This is why neo has no power there. Its not truly in the matrix world. If anything, its in the trainmans world.
It will be an interesting scene no matter what as we find out what purpose the child has.