Haha. I expected as much. I had the same thing. I asked platformio to list the settings, and it decided I really needed some fresh new libraries. It’s broken behaviour. But I don’t know what’s going on, or have the time to look into it.
Are you sure you’re not experiencing the same issue as I had, multiple installations? I’m asking because this issue is about disabling auto-update, suggesting your installation would be auto-updated, and if that would include pio itself, you should not see the “There is a new version” message. Which is the same issue I had, multiple installs.
PS: Pio is Open Source and mostly Python, which is really easy to read. It might be worth the dig into the source code to check where these settings come from/are stored.