Cannot set parents for pre-existing sims

I'm having this issue. I thought at first it was a mod UI issue,  but from looking around this sounds like its a consequence of the family tree trying to fill in gaps the player has not controlled. 

I took out my mods, deleted my cache, repaired my game typed in the necessary cheats and this is still happening.
I cannot even change the husband and son into household plain members, I click on it and it does nothing. 

Phantom parents keep popping up in the family tree and family relationships in general just keep moving around when loading in and out of the game. for example Jacob is suppose to be the son of the founder not his wife, (the daughter in law became the daughter) this happened after I reloaded into the game. It's completely ruined several families in my save.