How much different?
I'm guessing that, perhaps, the splits are different after the run because the AW/iPhone does some post-processing to the data during the transition from AW to iPhone. I know that some post-processing happens because the Activities app on the iPhone will show elevation even on workouts with the AW (series 2) only. The Series 2 doesn't have a barometer for elevation, so it must be done afterwards using the map and geo-data.
Maybe the post-processing also looks at your actual location at the mile splits and adjusts them to the map, wheras during the run, the AW just tracks differential between the GPS data points.