While everyone is looking up to space, other planets and the rest of the universe, there is a whole world buried directly underneath us...
Mods introducing new content into the game.
Map generation and terrain modification.
New Ores and resources as well as machines.
Subsurface is forcibly rewriting the map gen while it's in the modlist, I have a islands gen setup and it reverts it to default upon exiting the starting chunks
the map gen settings for the subsuface is probably accidentally being applied to the nauvis surface level
Same issue was on GitHub (https://github.com/NathaU/factorio-subsurface/issues/6) it is fixed for the next release