I’m wondering whether it might not be related to the game being V-Synced. Perhaps the game itself completes an update in much less than the 0.0166s required from 60fps–but every so often something causes a momentary slowdown. This results in an unusually-long update, one that ends up finishing just before the next screen-refresh. But because the game’s updates complete quickly, that’s enough time for an update to finish, and thus the long update is followed by a very short update, before a return to the usual 0.0166s-updates.
However, this is all very speculative on my part.