My original gyn, who first diagnosed me, firmly believed there was an immune system issue at play. He told me that when the back flow happens, the body should react to the lining being in an incorrect area and attack it. However, with endo, the body doesn't attack it and it grows. I believe there is some truth in that as I have a history of having a somewhat lowered immune system.
Its not the only cause of endo, but i have heard of reflux menstruation. My sister-in-law gave me a book "The Endometriosis Answer Book: New Hope, New Help by, Niels H Lauersen, M.D.,PH.D and Constance Deswaan". It talks about Reflux Menstruation. I have ovarian cysts that rupture every month, and endo. The endo was either caused from my cysts rupturing or when i had my c-section. If u can find the book, i highly recommend getting it and reading it. It has helped me understand the Endo alot.