Sub-assemblies in BOM have always been like that - It would be awesome if you could just show sub-assemblies, or be able to hand pick what you need. You can somewhat by using the indented BOM and showing/hiding the rows you don't want to show..
The problem I'm having is new. Yes, you've always had to change the "show" /"hide" option in configurations to suit your needs, but I've never seen it where changing the option from "show" to "hide" has caused entire subassemblies to disappear altogether. In the past, making the change did what I wanted it to. The subassembly itself appeared on the BOM, rather than the subassembly components. The problem I'm describing is one where not only do the components disappear, but the subassembly doesn't then appear in their place, as if it were excluded from the BOM. Again, this doesn't happen all the time, but it's happened twice recently, and never before then, at least not for me.