I have had this happen also. Sometimes it uploads right away and other times I waited for almost a whole day before they showed up. In flight data manager program he talks about this problem even with the Bebops so it seems to be a Parrot server problem. Here is what Kenth Jensen had to say about it.
"
Missing flights from Drone Academy?
In order to get flight data to be uploaded from the Parrot Bebop to the Drone Academy, make sure to re-connect your phone / tablet / iPad to your wifi Internet after the flight is completed.
If you are using both a SkyController and a tablet / phone, Parrot have currently a bug where flight data is very often not uploaded at all.
The bug is reported to Parrot and they have acknowledged it, they are working on fixing this bug.
In the meantime the following workaround can be used:
1: After landing, keep the FreeFlight App, the Bebop and the Skycontroller running - do not press the "Record" button for stopping the recording.
2: On the Freeflight App, go to the home screen by pressing the "Back arrow" pointing to the left in the upper lefthand side of the screen, now the home screen appears and you can see that the flight data is transferred to the tablet, and will go to Drone Academy after internet connection is restored
You can now turn off the FreeFlight App, the bebop and the SkyController.