Mine were working fine until I updated game via the opt-in patch (no blame, just an observation).  I simply deleted my faction and built it again just in case there were some .XML changes I wasn't aware of.  Everything is working fine again.

Select the portrait you want and press add male or add female.

so my face has frogs for males and squirrels for females...

dont judge me!

Tried this with 3 civs now and this feature is broken for me. All the portraits are appearing, and after clicking add male/female are appearing in my portraits just fine. But in game they never work, just the human faces and names come up, never mine. 

I am using it..Just have to drop the citizen portraits into the faction/citizen file in your docs then add them in the civ builder along with editing the names xml

Jane, its been over five years, so my memory is really fuzzy. Did you update your xml file so it knows where to look for the photos? I think as long as you update that, they should show up during your custom civ creation menu where you add them in from there at the beginning of each play thru. Also, I think you have to tag them male and female some how, maybe in the xml file. 

so an xml file is a text file used for organizing things, kind of like a text version of a spread sheet. They use tags like old school html.  youll need to find it and open it with notepad or better yet download notepad ++. Then in the file youll see the npc portraits , and you just add yours in a similar fashion. Sounds complicated but you can figure it out