Hapiness

That explanation was not the result of extensive tests, but, rather, a theory that I came up with in the back of my mind and never saw contradicted in any of my experiences. In particular, it gave a reasonable explanation of why Mike's Chapel is ineffective at deity plus 3 and 4. That being said, there weren't that many times when I was checking the effects of contentment structures, because I stopped building them and relied on a 40-50% luxury rate.

Black hats exhibit strange behaviors. If you have 2 left over after luxuries, Bach's may not fix them. If, however, you move a unit outside your city, the 2 unhappy faces will turn your black heads to red, which can then be fixed by Bach's! I once captured the city with Shakespeare's Theater at deity plus 3, and it would still have unhappy (but I'm not sure if there were any black hats) citizens after all was applied (in the absence of luxuries, of course). Another (slightly less) strange thing is that the happiness window and your citizens at the top of the screen don't always agree. Sometimes, the citizens above your worker allocation tiles will be red, while the last row of the happiness window will show them black.

Given these strange behaviors, the observation that my theory on the subject isn't entirely accurate isn't all that surprising, nor is the fact that another anomaly exists. You might try checking if the cities suffering more unhappiness happen to be the ones that are penalized extra by the riot factor (I'm pretty certain the find-city option lists all the cities in order, and you are probably far enough into the game that you have seen all ai cities).

I haven't really cared to look into the matter of black hats further, because I doubt that there is a discovery that can be more cost-effective to deal with black hats than luxuries (and Bach's). Also, the last D+n game I played was whatever the last succession game was.
 
You might try checking if the cities suffering more unhappiness happen to be the ones that are penalized extra by the riot factor (I'm pretty certain the find-city option lists all the cities in order, and you are probably far enough into the game that you have seen all ai cities).
My black factor is between 8 and 9. For a city of size 7 or smaller whether it gets hit by 8 or 9 is immaterial. I should see black+ citizens. I looked at all my cities and 9 of them have black+ citizens. All are under size 8. Here is the data:

City size, number of cities of this size, how many have black+ citizens
1 9 1
2 2 2
3 3 3
4 3 3
5 3 0
6 1 0
7 6 0
 
Here is yet another anomaly: If I employ an entertainer in a city with all blacks, I expect one of the remaining blacks to turn light blue and others to remain unaffected. I tried this in all my cities of size 3-7 and noticed that in 4 cases (my 3 cities of size 5 and my one city of size 6) I get a black turned red on top of the expected effect. In other words:
City before entertainer: b b b b b
City after entertainer: lb r b b e
 
My black factor is between 8 and 9. For a city of size 7 or smaller whether it gets hit by 8 or 9 is immaterial. I should see black+ citizens. I looked at all my cities and 9 of them have black+ citizens.

I realize that. However, black hats behave strangely sometimes (as I tried to convey), and, in the absence of further insight, I thought it might be worth checking. Given the fact that having lots of black hats was probably considered rare by the creators of the game, the implementation of the mechanic might behave strangely for lots of black hats.

You have a few options at the moment:
a) Increase your luxury rate (or increase trade) or station military units outside your small cities and stop worrying about this.
b) Run a few tests on the matter to find out exactly how black hats are calculated by the game (as far as I know, cheat mode doesn't impact happiness in any way).
c) If I don't get to it sooner, remind me in December (when I'll likely have more time) about this and I'll run some tests myself.
 
It is not a real problem in my game, more of a nuisance that caught my attention and I decided to spend some time figuring it out.

Obviously this is another area where more research is required. Hopefully we can cooperate on this.
 
I have not much to add except for the fact that the large map bonus also does not apply to an old game of mine, which was played with the Europe map (the one that came with the game) It was the size of a standard large map.

Since both of them were player-made and not randomly generated, maybe the MapSize factor is void for maps that went through the MapEditor.

Another interesting thing is that when I digged up an old save from GOTM 119 (which had a 100x100 randomly-generated map, but the Spanish starting position was modified a bit) and did some calculations, the MapSize factor also turned out to be absent.
 
Given what you say, my guess is that the map size factor is tied to one particular size, 120x75, that the game considers large. The program probably checks for that size and if it does not find a match considers the map not large.
 
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