In PHP > Quality Tools > PHP CS Fixer: Make sure it is set to ON. Also click the "..." next to it and click "Validate" to ensure PHPStorm is using it properly.
In PHP > Quality Tools: Make sure "External Formatters" is set to "PHP CS Fixer"
In Editor > Inspections: Search for "PHP CS Fixer" and make sure it is selected. Also check the Severity and Highlighter Settings. Generally you'll want this as "Weak Warning", but can be set to whatever you'd like
That's everything I can think of.