So, I checked with my version of Wonderdraft (currently version 1.1.6, I skipped the Update to 1.1.8 just in case if this is your problem):
I created this directory
C:\Users\(user)\AppData\Roaming\Wonderdraft\assets\A Fistful of Darkness\sprites\symbols
I unzipped the files and put them there
--> subdirectories "aFoD Cliffs", "aFoD Landscape" etc.
NOTE: I did not edit any metafiles, I just placed the files there and that's it.
I started Wonderdraft, created a new map (theme black/white).
I selected "symbols", selected "aF oD Settlement Town" and placed some icons on the map.
I exported Image=Normal, Format=PNG (unselected Export Trace Image).
Result: everything's ok. Another export with Format=JPG was also fine.
What's different on your side?