Have you changed your water level settings? Specifically, do you have more than one water area with different levels?
I realized yesterday that my code that breaks the mesh into regions wasn't nearly perfect, and I've learned a *lot* more about how the collision tree really works. I'm currenly rewriting how the tree is built (I'm trying to do it the right way this time).
Try setting all your water/lava areas to have the same level, and let me know if that helps in the meantime.
WC
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