The two iPhones appears in iTunes but the run data is not synced with Nike+
Humm, this is weird, mine does ok, but I never tried with both on iTunes... always one of a time.
I did found several forum discussions regarding the out of sync with Nike Plus, and this is from Aug 26th and already have 8 pages :o
it describes plenty of out of sync workouts (maybe it's an app bug)
probably is a good idea to post on Nike forum as well.