I'm right though? It was previously established that the incarnation before the newly regenerated Eccleston was the one that ended the Time War. We assumed it was Paul McGann, but it's John Hurt.
Explain where the problem lies?
is saying is that the ninth and tenth Doctors were painted by what he had done during the Time War, but the eleventh Doctor says the Hurt Doctor did things that made him anathema to his perception of himself, so there's a disconnect in the Doctor's self-perception of his role in Time War if the Time War is being dumped onto Hurt.