To reproduce: 

Follow these steps:

1. Extract the project I have attached and open it in Visual Studio.
2. Run it.
2a. You should note two docked windows on the left (tabbed).
3. Click on the "Open Next Window" button.  The first two clicks will simple open the first two docking windows (already open)
On the 3rd click another docking window should appear on the right.
Click the button a couple more times.  You should have 3 docked windows on the right.
4. Now, drag the windows on the left so they are floating and docked together.
5. Click on the Save Layout button at the bottom.
6. Close and rerun the sample.
You should note that the floating windows appear at the expected location.  Move them off to the side away from their default location (away from the center of the screen)
So far so good.
7. Upon reopening the application with toolWindow3, 4 and 5 floating and docked close the floating window.
8. Save the layout.
--> This is where the key is...
9. Close and rerun the sample.
If you watch quickly you'll see several windows "flicker".  They appear and disappear quickly.
Now, if you hit the "Open Next Window" button 5x, it will open the first two (already open) and then open the 3rd, 4th and 5th windows.  But NOTE - they are NOT docked together.  They are also not at the location where you left them (remember you needed to move them to the side)