Sorry for not replying earlier.
I believe this is a pre-existing issue and is not related to updates that we did, but it can easily be related to the overall mesh part usage in your game. Basically we have the issue in the current clustering system where when we can't keep all meshes you have in the mesh cache all at once - the mesh cache is capped to 96 MB which is around 1-2 million vertices - you get cache thrashing issues similar to what you describe.
We're working on rolling out a new, more efficient rendering system for CSG/MeshParts that does not have this issue, hopefully it would be live in a month or so. I'll take a look at bumping up the cache limit a bit in the short term, but also that's a lot of mesh data that you're using (the game is awesome though)