Apple submitted evidence (receipts) proving that they had purchased the chip from Intel, who had in turn already licensed the patents from Samsung[1]. A business cannot demand payment for a patent license twice. They also cannot dictate who the patent encumbered products may be sold to. This is not a matter of opinion, it is a matter of simple fact. If Samsung do file a JNVO, then it will be thrown out with prejudice for that reason.
[1]Known as patent exhaustion - http://en.wikipedia.org/wiki/Exhaustion_doctrine