Is there something in RFC that stops religions being founded in your capital if you have more than one city? I'm playing the Romans and gave myself a Great Prophet because I was sick of India beating me to Theology but every time I use him to learn it the holy city goes anywhere but Roma. Am I wasting my time or do I just need to keep putting off using it until one turn it randomly picks Roma to found it in?

why dont you just change the holy city in wb too?

Mainly because I don't know if that will have any unforeseen consequences but my question stands even without my nasty cheating ways. In all the games I've ever played I can't recall ever founding a religion in my capital after I had a second city.

a religion is most likely to spawn in your newest/most underdeveloped city (in the normal game too, since vanilla), but i guess there is a very small chance it may spawn in your capital (though it might be so small, i wouldnt try to save and load)

it will only be in your capital if it's your only city.

It's in the base game as well. I don't recall the exact probability formula but it goes something like:

Each city gets a chance to be the holy city, which is increased by its population and decreased by the number of religions already present in the city, and if the city is a capital then its chances are divided by a factor of 8. This makes it extremely unlikely for a capital to found a religion when you have multiple cities.

Edit: see http://forums.civfanatics.com/archive/index.php/t-241290.html

interesting.
I may tweak the formula to make it more realistic in the specific cases of Christianity and Islam.

Yeah, as the Arabians I was getting Aden, As-Sur, and Dalmun as my Islamic Holy City instead of Mecca a lot of the time. Mecca didn't have another religion spread to it, either.