To reproduce:

1. Open attached project.
2. Play "test" scene.
3. Look at the Console window. You should be getting "Invalid AABB aabb" and "Invalid AABB rkBox" errors.
These errors happen most of the time, but not always.

Expected result: Scene stays as it is.
Actual result: Objects with "Configurable Joint" get their XYZ Position changed to NaN. "Invalid AABB aabb" and "Invalid AABB rkBox" errors appear in a Console window.

Workarounds:
Select all "JointHeadpiece" and change their Scale from (-1,1,1) to (1,1,1).
or
Select all "JointHeadpiece" go to their "Configurable Joint" component and change "Angular X Motion", "Angular Y Motion", "Angular Z Motion" to Free.
or
Select all "Cube" objects, go to their "Configurable Joint" component and change "X Motion", "Y Motion", "Z Motion" to Free. (but then cubes will fall).
or
Avoid some Rigidbody.AddForce values in the script.Error happens when both X and Z values are non zero.

Reproducible with: Unity 5.4.2, Unity 5.4.1, Unity 5.4.0
Not reproducible with: Unity 5.3.6 and older

Fixed in Unity 5.5.0