In the stripped down file I uploaded, the 3 (approximation of) nuts, can be shut off from two non-nested layers.
As much as you may try to move them, they will continue to respond in this fashion.
I sometimes make groups of instances; I wonder if that might be causing Rhino to get confused. It still looks like a bug to me.
I am considering moving everything onto one layer except for work and construction layers, but what am I going to tell people–that Rhino blocks are klunky to use or bugged?
What I want: to create a block, and then it basically be global, like a global variable, and then I want to be able to spawn an (local) instance on any layer from that (global) geometry that I can move to any layer I want.
I have also had problems with external file blocks that make me want to distrust them, though I want to experiment with them for making blueprints.
[BTW, my project is basically a grounds-keeping machine, which has around: 966 block instances, 20 extrusions, 103 points, 97 curves, 175 polysurfaces, 17 surfaces, 1 linear dimension. I have tried to keep good organization in this project. Perhaps I can distort/adulterate the file dimention-wise so that it could be studied.]