Those timers have been started simultaneously.
Filter gates are set to 200sec. So 3x200 sec should be 600 sec, so should be 1 cycle.
Here it is, look where is the cycle timer when filters have reached 3x200sec... Only a third of the cycle has passed.
The more lag there's on the game, the more shift it seems you get. I've tried with a freshly created map and didn't noticed it that much.
Save joined. Just reset both counters, reset gates, and you'll very quickly see it.
That's quite a big one, if all delay-gate are messed up. Just note I didn't tried with buffer.
Load my save, or use the design shown on an heavy save