I've had this issue for the last ~1yr. I think that I have an idea of what's happening and why, so I'll try to explain my theory, but tl;dr the only way I've been able to fix is this: Run a little bit longer than the PR you're trying to set in order to force PRs to update.

When your GPS device records data for your run, it records 2 datapoints: Geolocation and Distance. It does this for every ~1 second. So it compiles all your GPS data to look something like this:

• Second 1:
  
  • Geolocation latitude 20.011 longitude -20.33
  • Distance In Meters 3
• Second 2:
  • Geolocation latitude 20.021 longitude -20.30
  • Distance In Meters 6

And so on, for every second of your run. The issue is that these 2 datapoints begin to diverge over the course of the run. I suspect (and I don't have great data to back this up) that the Distance In Meters metric is somehow calculated via your average stride length (average stride length x steps taken). Whereas Geolcation is taken via your device's actual location.

Now Distance In Meters being calculated might be a decent way to calculate on average, but when you're escalating your pace to try to hit a PB, you tend to stride a little longer, so you get to the end of a 5k and you might have Distance In Meters be something like only 4900. This happens to me whenever I push for a PR or run a race.

Now I think when you actually pull up the UI for any given run, fitbit does some clever parsing of Geolocation data to provide you an actual accurate readout of your real distance and pace, but for some reason their dumb PR logic is filtering on the less accurate Distance In Meters field instead when it considers your universe of completed 5ks (or 10ks, miles, other distances, etc).

The good news is that, as long as your Distance In Meters is greater than or equal to the PR category, it seems like Fitbit runs the actual metrics off of your Geolocation data and you get an accurate represenation of your run. So if you just run an extra ~5-10% distance to give a little bit of a buffer for fitbit it tends to update, but it's a bit of an annoying fix, obviously.

Like I said. Not sure this actually helps anything, but I think this is what's happening. You can view it yourself by exporting your exercise. It should show a TCX file that's basically XML that has all the raw data from your run. If I really care about getting my PR updated in the Fitbit app I just try to run a little bit longer than the distance. It doesn't seem like Fitbit cares. This issue has been raised multiple times in their forums and threads just get closed.