August 2022 and this is still happening, rebooting doesn't help make the popup go away and neither does clicking Do Not Reboot (the popup just comes back). When I check the endpoint profile's XML, vulnerability scan is already set to 0 so I have no idea why it keeps trying to scan endpoints in the first place.
Update in 2024: This is actually related to the Windows Update thing in the SSL-VPN config. Disable that and these popups should be less frequent.