After updating to 1.3.2, I find a lot of shrines all over the place in new generated chunks.

I assume this is not correct.

My config changes are:
ancientshrine and desertstructure I:Chance=160, smallshrine I:Chance=200

The S:idealDistance value is set to default values.

Minecraft: 1.10.2
Forge: 12.18.3.2254
Astral Sorcery: 1.3.2 beta

I also use mods affecting the world generation, if that matters:
Biomes O' Plenty: 5.0.0.2162
GeographiCraft: 0.8.7
Realistic Terrain Generation: 4.1.2.4

First report for the Issue in question: #121

You might've used one of the versions that already got deleted again. There were 2 versions of 1.3.2 uploaded before the current one which had that bug.

I tested without other mods, just Optifine and Astral Sorcery, and the issue still appears.

Well, I downgraded to 1.3.1, the issue was gone, then upgraded to 1.3.2 again and the issue is still gone. I'm confused... maybe I made a mistake updating the config in the first run...? Nevermind.