So thanks to the season 5 amazing finale, we now know who the amazing Jacob is.
I loved his character. Thought he was so awesome in this nonchalant way. Mark Pellegrino did amazing.
Anyway, We now know that Jacob has lived underneath the foot of the statue. For how long he has lived there is Debatable.
But for the point of my argument lets say he has been there since at least 2004 when the losties crashed on the island.
When Ben takes Locke to the cabin and John sees that really quick flash of someone and he hears a voice say Help Me, who was it? and who's eye was that in the other episode where hurley encountered the cabin?
With the ashes always around it, I think Jacob or someone else has sort of banished The nemesis into this Cabin, and that ash has served as some kind of barrier for his physical Body. Which is why when llana discovered that section of ash missing she looked worried and said someone else has been here, and burned the cabin.
So, to me, if it was the nemesis , the words Help Me would make sense spoken to John Locke. Seeing as how John Locke's body helped him Kill Jacob. Supposedly.