You can easily calculate your own true average MPH by dividing your mileage by your actual clock time.
What these apps are doing is trying to boost your average MPH by automatically cutting out "stopped" time, ie at red lights or bathroom stops, etc. I bet they have different algorithms for guessing when you are actually stopped, though. They may consider you to be stopped when your speed drops below 3mph or 1mph and you may have to stay below that speed for some amount of time before they consider you to be stopped. For this reason, all of the results you get are at best rough estimates. The only easily verifiable average MPH is the true average, not trying to boost your speed by eliminating stopped time.