ok. Getting weirder now.
As I create drawings of the lower level sub-assemblies, the BOM appears to be working correctly. The two subassemblies here are held in place by 3 screws at the hinge.
This seems buggy. The only difference between this assembly and the top level assembly is that I have put the fasteners in a folder. I've taken them out of the folder and the top level is still incorrect.