I experienced this too before. Then i restarted the game and it suddenly went smooth again - then 30 mins later it started to stutter again.Geez, this latest build really does run like shit. And I never had a problem with any of the earlier builds. But no biggie, there is nothing new that's relevant anyway so I'm just going to restore the previous version.
What i found is the reason is CPU-"leaks". Don't ask me how it's possible, but when i play the latest build and look at my afterburner stats, cpu-usage keeps constantly rising over time - on my graphs it literarily looks like someone put a ruler to the cpu-peaks on all my cores. Something is consuming ever more cpu-ressources as you play, until the game starts dropping frames NOT because they don't render fast enough, but instead because the gamelogic cannot keep up.
My guess from the behavior of other gameengines is this: Once the game is CPU-bottlenecked, the physics engine can no longer keep up, so it drops rendered frames until the physical representation of the world is ready for the next frame. This is why you see no framedrop in the FPS-counter, even when the game is skipping every 2nd frame: The FPS-counter only counts RENDERED frames, not actually DISPLAYED frames, which is very confusing to say the least.