Breakthrough! I think I figured out the diplomacy bug, the Egypt diplomacy bug, and another suspected bug that had been bothering me (difficulty level).
When you set conditions or the game, you're not setting them for the human player. You're setting them for Egypt. Egypt is always counted as the human player, while the human player is considered an AI. This bugs diplomacy, and, when I was trying to play on Viceroy to test the game out, Egypt always founded religions before their intended founders because it was Egypt that was getting the bonuses of Viceroy, not my civ.
Why Egypt? They're player 1. I'm no great shakes at coding, but the solution would be either to set the human player to always be player 1 or to figure out how this coding is different from the way it works in default RFC, where the problem doesn't exist.