Could you please post a screenshot of the automation you are using?
Also, how are you setting the system to disarmed? Because there was a change in design philosophy between the classic app and the V3 classic app and you can no longer change the security.mode based on Geopresence. See the community FAQ:
Finally, SHM in the classic app and smartthings home monitor (STHM) are two completely separate sets of code. If you have an automation set up under the classic app to change the armed status, it does not change the status that shows up in the new V3 app, and vice versa. So that can also lead to considerable confusion.