Wow that's pretty fantastic. I have to wonder though if this is more due to you being in a giant swamp biome. Your lake setting should have just made the small pools of water that generate less common. I'll have to check this out when I get home.
This has nothing to do with water lakes, which should never generate in lava (conversely, you never see lava lakes in normal oceans); it is due to how swamps generate, adding random areas of water interspersed with bits of land so there is a less distinct transition between land and water. The same code also ignores the sea level setting, always placing this water at y=62 (63 sea level).