I think I isolated a way to reproduce this bug. It has to do with faction rep being high for 2 or more factions at the same time.
I picked the game back up to try the new DLC, opted to play normally by siding only with one faction, and never saw this bug while I completed the game for the first time.
Assuming the bug was fixed, I started a new game without the DLC and played normally, which means trying to get all factions up to 50-51% rep. Once I had Anu and Synedrion both over 50% rep and had raised New Jericho to the mid 20s, the bug reappeared.
Guessing I have to try selectively raising and lowering rep one faction at a time next.