Auto-switching is a feature of FlightCheck that “detects the type of file you are preflighting” and selects the proper Preflight Mode. If you preflight a QuarkXPress or Adobe InDesign file, FlightCheck will use the Non-PDF Preflight Mode Rules.
If you preflight a PDF file, FlightCheck will automatically switch to the PDF Preflight Mode Rules. As of FlightCheck 6, this feature is set up for you by default. (In earlier FlightCheck versions, you may have had to manually set up this feature.) The setup for auto-switching is found under the Advanced Preferences area.