I don't use the mod, but I saw someone on reddit with this issue, and determined Waterfill is causing it:
https://www.reddit.com/r/factorio/comments/1gsr0po/my_new_chunks_generate_like_anyone_know_how_to_fix/
I do not know what the collision mask on water & deepwater should be, but whatever you changed it to allows decoratives to start spawning on water. You could try these:
/c game.print(serpent.block(prototypes.tile.water.collision_mask))
/c game.print(serpent.block(prototypes.tile.deepwater.collision_mask))
In vanilla I see 6 collisions (doodad, floor, item, player, resource, water_tile) but the mod changes it to only 3 (player, resource, water_tile).
