The OOS logs alone were that big, or zipping the logs together with the save was that big? Will try to check it out sometime soonish. Just 2 human players, right?
Autoacquired promotions will show up as soon as the unit MOVES to a tile where the promotion is valid, or starts their turn. In the case of NoxNoctis, it is actually 2 AA promotions combined, so depending on the order in the XML it could require 2 triggers (start of turn + movement within borders, or 2 turn starts). There is some AA checking when a unit is built, but same issue, order in the XML could lead to needing 2 passes to get it done right (Creation + turn start). Making these checks happen at EVERY possible case where you can suddenly meet requirements would make for a rather insane processor hit unfortunately, the current implementation is about the best balance I can think of for speed + transparency.
I could have sworn I set it up for this last patch so that invisible units could capture unguarded cities. Were there workers in it or anything? That would mess it up for how I coded things I think. But yes, reveal yourself and you should have no issues. No need to play with movement since you can willfully drop Esus invis any time you want to though...