Recently, an update to the game changed modded factions to now require an additional line in an XML file to set the number of settlements for a faction. Without this line, the game will only generate one settlement for a modded faction. Some race/faction mods have updated and added this line, but many have not. If you don't want to wait for all of your favorite race/faction mods to update, you can edit in this line yourself. Here's how:
1. Navigate to the folder located here: \Steam\steamapps\workshop\content\294100\[MODID]\Defs\FactionDefs and find the file Faction_[NAMEOFFACTION].xml
the modID is the long number located at the end of the URL for the mods steam page.
2. Open the file with any old text editor (notepad will do) and paste in the line
<settlementGenerationWeight>1</settlementGenerationWeight> UNDER the line
<requiredCountAtGameStart>1</requiredCountAtGameStart> and save.
You can even change those numbers to have more or less factions, or bases per faction.