I seldom ask for help any more because my investment in SCP and SCPCC work so well. I write you as a huge hurricane is heading toward my home in Florida...there is nothing to do now but wait and use the time to survey my websites.
I have one site that is reporting back to SCPCC that it is still running Joomla 3.9, however, it is actually running 3.11. The site's SCP reports 3.11 but the Control Center doesn't see it. All other measurements are being reported accurately.
I really hope you and your family are fine. All my best wishes for the next hours...
Regarding to the Joomla version, it's really odd. When you launch a 'refresh' task Securitycheck Pro use the same method that the core uses.
Is there any caching system in this website? Also go to Extensions -> manager -> database and fix any reported errors. Sometimes database schema doesn't match with installed version.