Okay I'll be back on this
Stumbled upon a minor issue though.
I reopened the scene, and as I wanted to render the camera with the lens hidden, I had that same problem
The test scene "hiddenInstanceBug" I provided now works indeed with mti last release, but my 5D scene got some additional "groups complexity" that may cause problems with those screws.
You can see that the ones inside the hidden "lens" group get rendered, as well as some instanced cubes, that don't even have instances in any other part of the scene.
(They don't get into the render if I hide the actual objects again inside the hidden group)
Here it is: