Okay I think I understand what is going on and will look into fixing it. From what I can see, the terrain type bias completely controls how much of either jellynut or yumako patches spawn and does not update until the bias is changed and the map is re-randomized. For a temp fix, just keep the terrain type bias in the middle to ensure both spawn.
As for the fluids missing, that is a known bug. I have no idea what causes it, and from my previous testing, the fluids change from save to save all on the same version. I just used the mods lavafill and oilfill for the missing lakes on each planet.