lostwizard
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That seems to have resolved it.
Judging from a couple other posts since I made mine, you may have a more general issue related to how you flag the patched versions in CVEs. In all of the cases, it’s off by one and marking the patched version as still vulnerable.
I synchronized and re-ran the scan. It cleared the problem.
suPHP_ConfigPath is *NOT* required to point to the directory where .user.ini is located for .user.ini to be loaded. All adding it does is cause unneeded problems in exactly this sort of configuration by needlessly overriding whatever default php.ini path has been set up in the server configuration.
Edit: suPHP_ConfigPath only sets where the php.ini file is loaded from (by setting the PHPRC environment variable). .user.ini comes from the directory the script is in or any parent directory up to the document root: http://php.net/manual/en/configuration.file.per-user.php