If I put her in her 'Nude 1' outfit she has male parts, but if I select 'Change Sim' in a mirror and deselect all her clothing, she's got a female bottom.

I'm still getting the same issue with a Female Young Adult that I downloaded off the gallery-She's full Futa. So I've done all of the above with your nude mods (removing the old, adding in the new) I've even gone so far to delete the mosaic and nude skin details that you and Moxie made and re-download them again, opening the game between each new change I made.