If you don't edit the startpos correctly TWS2 will use the vanilla version, so that would explain why the new regions are missing. To fix this problem I recommend the following.
1) Make a mod and check that the new buildings work correctly.
2) Try adding one new building to my startpos. If this building doesn't work try adding a different one to the same region. In ETW the buildings were assigned a specific type in the CAI_World building_slot information, so you couldn't simply turn one building type into another building type. It's possible that something similar exists in TWS2.
Below is how the building types were classified in ETW. I recommend only trying to turn a building into another type of the same building. For example don't turn a building that produces the trade resource iron into a building that doesn't produce a trade resource.
0 = settlement building
1 = road or fortification
2 = town
3 = port
4 = non-trade resource building (iron, gold, gems)
5 = farm
6 = single trade resource building (timber, fur)
7 = multiple trade resource building (sugar or coffee, cotton or sugar)