I get small variations in pace between apps. It's usually due to the time being of by a second or two. Or the distance is of by a few tenths of a mile.One thing that has frustrated me though is that different apps have given me different paces. I use my watch with the built in workout app for a run, and it will give me one pace....use RunGap to upload that run's data to RunKeeper, and it will give me a different average pace, as much as 15 seconds difference.
The pace is usually within a few seconds. Nothing significant. If you're seeing a difference of 15 seconds, perhaps one of the apps isn't recognizing a pause.