Pics 2 and 3 appear to be from somewhat earlier in the game. Was there a wonder in the city at that time? If not, that is why it is not showing up...
If you turn on the "all other buildings" value, 128, what I think you will get is some big empty plazas and fewer buildings showing up in the city. The reason for this is that most buildings in C2C do not have any model to put on the map, but the city building layout code doesn't skip the no-model buildings so it picks buildings to show and then shows them - which means it shows nothing but the underlying city texture in most cases, leaving an empty space in the city. It also sees that there are a ton of actual buildings in the city so it adds fewer of the generic buildings from the city set which leaves the city with fewer buildings showing overall (with 128 off most of the buildings you see are generic filler buildings from the city set it is using).
I can see 2 ways to avoid this.
1) Define models for a lot more of the buildings.
2) Modify the layout code to not pick buildings that don't have models defined for them, if it can avoid it. Probably also counting the buildings that have models instead of all the buildings in the city when determining what percentage of the city should be real buildings vs. generic buildings.
That is assuming my vague idea of how the city layout works is correct...