@ts1depot - I'm also wondering if this behavior is a conflict of a mod. While I do play with NRaas' Story Progression mod, it isn't currently installed and hasn't been for a while. If it was, I would blame their behavior on that. Unless there is some residual effect from Story Progression removal, I can't think of what other installed mod could cause this.
The actual 'game modifications' I do have installed are designed to either promote things which enhance realism through choice like icarusallsorts 'Cook with Any Ingredient' mod or stop TS3 coded things which I don't want from happening such as bluegenjutsu's 'No Zombies' mod. Outside of NRaas' SP mod, I don't have another mod which opens their autonomy further.
A head scratcher this one is.