The problem is that you don't seem to have a clear PROBLEM in mind.
By your definition of morality only conscious choices - which cannot be dictated by evolution - count. So it can't be the choices themselves.
So the only way in which evolution can affect morality is if it gave us instincts that favoured behaving morally or imnorally. However, since you grant that animals can instinctively act in ways which would be good if they were consciously chosen it follows that evolution could provide us with instincts that lead us to favour a moral course of action over an immoral one. So it can't be that either.
So what, exactly, is the problem ?