I am having the same problem on my current .90 game, and I am doing a standard sized maze map, with normal game speed, I am also using Harbaal's civs. I founded Runes first, and spread it to a few civs, one of which eventually turned out to be my best friends, the Merfolk. I made sure every Merfolk city had Runes, in order to keep on friendly terms, and they adopted it as their state religion early in the game.
I also founded Leaves and Order, but avoided Veil and OO. Someone founded OO, and began to spread it around later in the game, within 50 turns or so of the founding of OO, eveyone except my civ and the Merfolk had converted to OO. It was about this time that I was shopping around for a civ to conquer (I had already taken out the Dark Elves), and settled on the Dark Dwarves (as we had the worst relations). Before I could declare on them the Dark Dwarves surprised me by declaring on me. They had the second lowest score, and I had the highest. I thought this would be a good time to leverage my friendly relations with the Merfolk, as they shared a land border with the DD, and I only had borders over the sea.
Just about this time, the Merfolk canceled their Defensive Pact with me, and I noticed that they had converted to OO as well. I thought that this was bery odd, as they had been the first civ I had spread Runes too, and they had been a Runes civ for hundreds of years. I thought I might want to patch things up a bit before asking them to decalre war on a civ that shared state religions with them, so I bribed them to convert back to Runes, which they happily obliged as I was offering them a juicy tech. A few turns later they were back on OO, and I could not convince them to change back to Runes (I wasn't willing to offer any bribes as I had been hosed on that before).
So it is just me with the Runes, and all 7 other civs with OO (soon to be 6, the DD have only 2 cities left). It would appear that some tweaking needs to be done to keep the later religions from becoming so dominant with the AI.
