Some items are always blocked, like the quarry/large furnace and refinery. Some are random like the large wooden boxes or the salvaged shelves. Is there some setting I'm missing?

I have it set up with BuildingOwners and Friends

Got some screens of what you mean by "blocked"?

I was coming back to update what was happening. I had changed from BuildingOwners to EntityOwner and it helped with most of the issues. Currently these are the only ones I'm aware of now.