Eh? What? I am beyond confused now.
I suddenly realized that my big assembly was inverted - it was a mirror image of what it ought to be. Also, it was much darker than it used to be. As if the lights were not falling on it from the right directions.
Puzzled, I clicked the "Orient → Front" icon in the Heads-Up view taskbar. The proper model snapped into view - brightly lit as is should be, correctly oriented and without that transparent surfaces thing.
I zoom out and in but the dark mirrored HLR/shaded thing is gone.
While it is nice that the problem is solved, the insanity of it all makes me sort of wary.
Just rerun or upgrade your video card driver and check.
Does your assembly have a Speedpak. Speedpack has an option to Ghost elements not included in the speedpack. Speedpacks will show surfaces of elements but not allow them to be selected. That might explain your quirky Graphical feedback in the Assembly.