" How does Boeing's use of these differ from these applications? "
It really shouldn't differ. You have x amount of stuff that you need to have powered by y amount of batteries. Question is, how is the cell being managed? Is it getting too hot? Is it not being properly charged? I have no idea....
Just take a look at the consumer Lithium rechargeable battery problems over the years, Dell had problems with batteries that were made in Japan and were of decent quality under well controlled manufacturing process... Stuff happens and sometimes we just don't understand it until after the fact...