LG Electronics vs Quanta Computers
My understanding was that the supreme court had ruled specifically against double dipping back in 2008 http://arstechnica.com/tech-policy/news/2008/06/scotus-keeps-lg-from-double-dipping-on-method-patents.ars and further defined the term 'patent exhaustion'
The exact details of the agreement between Apple Inc. and Lodysys are secret, but I'd guess that Lodysys hasn't deliberately slipped something past Apples lawyers.
What they may be claiming is that because App store apps are developed and sold separately to the phone itself then the point of sale of the phone doesn't cover the point of sale of the app, thus each app must separately license each patent.
The hollowness of this claim is that in-app payments are (by my understanding) included using apples API, code developed by apple and shipped in the phone as sold.