it could be those changes causing the weirdness, but the only thing I'm aware of that normally causes that is if those secrets share the same spheres, which i checked and there was only one instance of the same sphere being used twice (BLIGHT and disease which also erroneously used BLIGHT) and I've fixed that now. Never heard that bug messing with secrets that werent the culprit, but maybe it does. MASTER_A_SKILL shouldnt even allow secrets to appear, as the only reason mortals will approach gods to obtain a slab is to attain immortality, and that hasnt changed iirc since necromancy was implemented in the first place.
Fixing the duplicate SPHERE usage did not fix the WG crash.
oh, also, the issue with too many new civs showing up in worlds is because of the way the game places them, i.e. not at random or anything but selecting the first civ to place at random and from there going down the list and placing one of each until it loops back around to where it started. There isnt a good way to solve that besides removing the extra civs or duplicating the default ones (with new IDs) and injecting them at various points in the list. Which technically makes the list even longer. I tried alleviating this partly already by setting the new civs to only appear 1-2 times each via the max civ limit, so if two civs have already been placed it will skip over that entity and place the next civ on the list that hasnt reached its max civs limit, but that doesnt help on small worlds where you only have 15-20 civs being placed in total; it may not reach the end of the list at all.