Try a clean install of Sierra to an empty disk, see if you get this pop-up again. Don't use the installer you already have, download it from Apple here, this is the direct link for Sierra 10.12.6 full installer:
This is the support article:
This is the support article:
How to download and install macOS - Apple Support
Download and install current or previous versions of the Mac operating system on compatible Mac computers.
support.apple.com