The title says it all. To reproduce:
1. Go into a creative world.
2. Run:

/scoreboard objectives add isSneaking stat.sneakTime

3. Put in an always-active, repeating, unconditional command block:

effect @a[score_isSneaking_min=1] levitation 1 3 true

4. Put in another command block of the same type (higher on the y-axis than the first one, since that's supposed to make it activate later):

scoreboard players set @a[score_isSneaking_min=1] isSneaking 0

5. Crouch to fly!
6. Copy the command from the first block, destroy that block, replace it, and paste it back in. Same text, same block settings.
7. Crouch to... stay on the ground.
8. Wot.
9. Repeat step 6 for the second command block.
10. Crouch to fly again!

Very confused by this. Could it be related to MC-11193?