To reproduce:
/effect give @s speed 10
Look at the icon in the upper right until it runs out. Notice how it doesn't flash, even in the last few seconds.
If you really want to make sure, open your inventory and close it when there's a few seconds left. The effect icon in the HUD won't be flashing.
Tried this myself, seems to be working as intended.
Maybe client/server side lag is the problem.