My impression is that there are a couple of factors. One, I think, is that there were tensions within the LTTE movement that people from the outside could not readily observe, tensions between the Tamils of Jaffna and the Tamils of the east. He was the commander of the forces of the east. I have no idea of what the details were, but I think the frustration developed to such an extent that he decided he would break with the LTTE. When he went, he took a lot of people with him.
Also, my understanding is that he was traditionally very much on the moderate wing of the LTTE, so I think there may have been some frustration on that score.
No doubt, since he has now entered the government and when the Karuna forces left they started working implicitly with the military, there is clearly personal ambition as well.
I would think that there are at least those three factors.