Whiel this is a continuation of this thread http://newtondynamics.com/forum/viewtopic.php?f=9&t=5338&p=40723#p40723, I start a new thread for this because the title other title referred to an old issue that got solved some time ago already.
Sorry it took a few days, but finally, I colored the graph and show the number of units as well as upgraded to newton 2.16.

I also set up a copy of the live system for debugging purposes. You can get find it here: [url]wwwdev.confrontation-unlimited.net[/url]. Don't use the live system, it's still running on 2.12.
I created an admin account for you with credentials I send to you via pm. When you are connected to a region, you can press 5 and the debug window will appear you can see a few lines down. You can toggle the 8 graphs with the check boxes. They correspond to the 8 graphs newton offers.
I simulate the scene with 60Hz and every 8 frames, I flush the scene for determinism. That explains the spikes every 8 frames.
There is one region showing the current speed problem:

It's the region 15/16, you can connect to it in the dev system with your account. As you can see, it has >800 units and the physics take quite some time. Also note that they are just standing around and have nothing to do - but that's an abservation from the gamelogic point of view. If they are actually asleep or not I don't know. But compared to region 15/15:

There are less units but a lot more trees, which are static ellipsoids, the physics take a lot less time while the total amount of objects is only 200 less than in 15/16. So I assume, the units, the dynamic ellipsoids slow it down.