I see! Yes, that would explain it. I guess that means those types of items just are not grouped under any of the categories shown in the stockpile settings, and everything is removed when you click “none”, but these ‘hidden’ ones aren’t added back when you select “all”.
By the way, the fences have been disabled (as in, you can’t place them) while the team figures out a solution to the hovering-when-placed-adjacent-to-each-other issue. They also don’t seem to be recognized for trading purposes and such.