Ok, I haven't played since the latest patch, but bear with me.
Some games, I start normally. I play for a while, when I notice something strange. The offhand cities have a higher production rate than my capital, and this isn't a minor Fortress vs Town difference. I take a closer look, and see that my capital has a massive amount of unrest. Examine closer, and for some unexplainable reason, my own capital has the occupation unrest penalty attached to it?
As of now, I have seen this twice. Once, I was playing as Altair. The other and more recent time, I was playing with Umber. I lucked out, and got a special quest that eliminates the unrest penalty from conquered cities, and that included my capital.
Has anyone else ever seen this bug? I think I have the save file of both before and after the event for the Umber game, but I dunno. It seems unfair to start off with such a ridiculous disadvantage.