One thing that might cause confusion is that PWDF will allow you to overwrite pre-set map data, but there's no functionality to delete only the pre-set data. If you make a world using all the data maps, and then decide not to use a pre-set savagery map, the savagery map you genned previously will still be there even if you re-genned all the other maps. Make sure you're either using a clean param set with no existing map data, or make sure you're using all the data maps so that you aren't using garbage data from a previous map.
EDIT: One scenario I can think of is that if you check the box to use a PWDF savagery map, and then not bother to generate anything on the savagery tab, it will output a flat map with all the same value in every tile, which would likely prevent civ development.
EDIT2: Yeah, after a quick check, if you check the 'Savagery Map' box and not generate a savagery map, it will default to full savagery across the whole map which will stop civ growth. If you don't want to use a particular map, make sure not to check it's respective box. If you already exported a param set with it checked, and you want to still use that same param set without a particular data map, you'll have to delete it manually with a text editor.
The easiest thing would be to start with a fresh, unaltered world_gen.txt file, and don't alter the pre-existing param sets, instead, copy them by selecting the one you want to copy and typing a new name into the param set name field (Not exactly intuitive.). That way you can delete the param sets that you create without messing up the original ones. I probably should have enforced that practice somehow, but I didn't and I probably don't have time to make a major change like that.