The game looks at how far up you move when deciding whether to increment your jump statistic. This is probably so that if you can't jump (due to a high level of jump boost or levitation), it won't increment. However, it's possible to jump by such a small amount (with jump boost level 251 or by jumping under a trapdoor) that the game doesn't register it as a jump, even though you can see yourself move.
Interestingly, if you use jump boost level 251 in creative mode, you can get your jump score to increment if you double jump very quickly. The game just looks at the distance you moved right after the jump, and it counts your flying.
Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w43a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.