Hi Ash,
We appreciate your initiative trying to troubleshoot the problem. The control pop ups might be due to a bug or a driver issue. However, the problem shows only with a certain app so it can also be an app issue specially if it happens even when the cover is detached.
Have you tried to perform a two-button shutdown? If not, you can do this by pressing and holding the Volume-up button and the Power button on your Surface at the same time for 15 seconds and then release both of them. The screen may flash the Surface logo, but remember to continue holding down the buttons for 15 seconds.
If the issue persists, we suggest you proceed with reinstalling the Surface cover driver. Here's how:
- Select the search box in the taskbar, enter device manager, and select Device Manager in the results.
- Expand Keyboards.
- Right-click Surface Type Cover Filter Device.
- Select Uninstall > OK.
- Restart your Surface. It'll automatically download and install the Surface Cover driver the next time you connect to the Internet.
Give us an update, and let us know if you have any additional concerns.
Regards.