Okay, so this might be very complicated to understand/explain. Ill try.
First, I had a scoreboard objective set up that was a stat.jump objective to detect when I jumped.
Then after ran: /effect @p 25 1 250 and then made sure all effects were cleared I had to jump about 6 times before the scoreboard objective started counting my jumps again.
Now this is where it gets strange, if I apply levitation 250 (Or any high number) and clear it while I am under a ceiling the scoreboard objective will work as it is supposed to. This is a very important bug to get fixed as high amounts of levitation will be used quite a lot by map makers and minigame designers. So if you need any extra information please reply and ask for more.