Issue occurs when editing the World generation settings in game. I set stalagmites & stalactites to zero (to avoid overlap with quark) and it sets multiple other settings to zero as well. Always in consecutive pairs just like the stalactites/stalagmites. I can manually set these back to default using the buttons.

Hmm that doesn't sound right

The 1.12 version is no longer being developed, and stalagmites/stalactites are being dropped in favor of Quark's.