night owl: As a beginner you indeed should start on 9x9. It is more easy to handle.
the x's you are talking about are probably the marking of dead groups. When both players pass, the dead groups should be marked. Brainking helps a little with the marking. When one player disagrees (which should be expected as Brainking very roughly counts) he/she can offer a better proposal as to which groups are dead. This causes very different markings.
I hope you understand, else invite me for a teaching game 9x9.