I have had this exact same problem spring up on a few different macOS devices through the last several years.
Does it perhaps have something to do with the two separate pages of "Update" settings? Note:
- Under Standard Settings>Basic>General, there is a "Enable automatic update checking"
- Under Advanced>General>General Stuff>Updates, there is "Enable automatic update checking" and "Silently download & install..."
I've tried turning off most of these settings to see if the problem resolves itself.