I've got a mesh as an avatar and clone it twice to get red and blue avatar "prototypes".
Then I call createInstance on on the red-avatar the new mesh is ok and visible.
Afterwards I call createInstance on the blue-avatar (ok), but this has the side-effect that the first instance disappears.
It seems that the first time when createInstance is called on a prototype it somehow impacts the other clones. It did work on 2.3.0.
http://www.babylonjs-playground.com/#1VVRMK#2
BTW: Excelent framework, I love it !!!