When the world saves you will freeze for a split second up to 2 or 3 seconds depending on your rig. This happens to everyone. Next time you notice it check out the the top left or right corner of your screen (I forget where it is) and see if it says world save.

If that's not it I'm not sure what to tell you. The game isn't optimized yet and there are some really bad desync issues in multi player, as well as serious performance hits when you do a lot of land Terra forming.