In Lois McMaster Bujold's The Curse of Chalion, one of the primary differences between the Five Kingdoms and the Roknari is their faith. While both faiths worship the same gods, the Roknari Quadrene only worship four of them (Father, Mother, Son, and Daughter), while the Chalion Quintarians additionally also worship The Bastard. Is it known how this came about?
The Curse of Chalion itself doesn't talk much about Roknari theology (understandable: the only actual Roknari we meet, i.e. not just hear about from Cazaril's recollections, is a Quintarian). Paladin of Souls is where you're more likely to find an answer.
So it looks like the root of the schism was a disagreement about the nature of the gods, i.e. whether a demon can defeat the will of a goddess.
What I haven't been able to find is any mention of the history of the schism: the furthest back Bujold goes is Fonsa's struggles with The Golden General, which is only a couple of generations ago.