Not quite, it’s just there is a delay. If you wait about 5 mins they will sync up.
You can get around this by adding the switches that are created in SmartThings for the Harmony Activities as devices within the Harmony remote app. You can then set up commands for those switches in your Harmony Activity and the switches will update in real time in ST when the Harmony Activity runs. I don’t do this - I just live with the delay I mentioned before.