I agree that it would seem to be user error, particularly when you consider the fact that google doesn't return any references to anyone else having a similar bug. However, I have done everything I know how to get that checkpoint to register for me. There is no doubt I'm actually flying through the thing--I flew through the previous 8 or so without any problems, over and over and over. I can get 3-4 tries each time on that one before the mission cancels and I've tried the mission 7 times or so. Which means, I've attempted the thing
at least 21 times. I've tried it at maximum speed, at minimum speed, climbing, diving, stalling, upside down. The only other thing I can think of to try is just to assume the checkpoint is registering and land to see if the mission will end successfully.