First of all I would suggest going to Project settings → Engine → Collision and create some new Object Channels and assign them to your Cubes and to your 3D Structure so they don’t use the same channel which now is World Dynamic. That will make your life much easier.
Create a different trace for the 3D Structure and another for your cubes, derived from the same command line.
I believe that the fact that both (Structure and Boxes) are using the same channel, it confuses the trace believing the boxes are still in place when they have actually moved.