Ironically, I feel so bad when I order five things in one order (ship when everything is ready, free shipping) and them Amazon sends me five different packages at great expense, that I am almost relieved they are offering this.
How did that item get to the store?
They were probably at different warehouse/shipping facilities and Amazon figured it was better to just fire them off than try to unite them in one place. I find when I order obscure stuff - uncommon books, a Go board, whatever - it's more likely to show up by itself than if I'm ordering mostly bestsellers and popular books.