How does this mod interact with this (and other) storylines?

I've captured Seta and handed them over to authorities in Admag - now in theory (at least according to the Golem's dialogue) Bad teeth and Stack have 'fallen' to the Shek - but on the map they still show as controlled by the Holy nation.
Is this because I have this mod running?
Just to clarify this is the only mod of this nature I have running.
If I were to take any other town with this mod active, how would I achieve it?

Appreciate any feedback.