I understand that the Hep C virus lives in liver cells and the immune system attacks the virus killing it and the host cells. I believe that after many years, the immune system may start attacking the healthy cells as well which is the autoimmune hepatitis induced by hepC.
There may be cases where due to some malfunction of the immune system, it may start attacking the liver with no history of viral hepatitis.
If during treatment the liver enzymes go up instead of down, it is worth testing for autoimmune response. I had a test which showed a weak auto-immune response, but it was enhanced during IFN tx and I didn't respond.
I don't know if HepC is related in anyway, but here is a decent article about Autoimmune Hep.
http://www.cumc.columbia.edu/dept/gi/autoimmune.html