In apparently just one folder in my catalog, thumbnails in grid view have four different shades of grey:
The upper-right thumbnail is most selected, and the one to the right of it is selected. But why do the remaining thumbnails have two different shades of grey?
I have seen then when you expand a stack, the shade of grey is different than the non-stacked photos.
However, I don't see a stacking indicator in your screen shot
Great clue. Those darkest shade of grey thumbnails are in fact at the bottom of stacks, and the tops of the stacks are rejected and filtered out.
I think it's a bug that there isn't an indicator they're in a stack. When the bottom of stack is rejected and filtered out, the top-of-stack thumbnail has an indicator.
In a related comment, my impressions as a recent Aperture to LR convert is that there is too much grey in the UI. I recognize that grey is a great background to stay out of the way of the images, but in situations like above, it takes too much thought to know what is selected, deselected, marked for deletion, stacked, picked, etc...when all of these are variations of grey and white, it becomes a bit confusing. I am getting used to it, and while 95% of what LR does is better than Aperture, the "selection" UI one thing that Aperture does better. (In my opinion)