How to reproduce:
A: Run the "Scene01" scene in the attached example project and observe how cubes act
B: The setup explained below

Setup
A. Create two cubes, place them one unit apart
B. Attach a rigidbody to both, freeze position in the Z axis and rotation in Y on both cubes
C. Rotate both differently with low numbers in the x and y axis
D. Add a fixed joint to one cube and use the other as the connected body
E. Add a surface underneath the cubes for them to drop on
F. Run the project
G: Remove the Fixedjoint, then re add it, the problem persists