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The old school yellow funnel is really bad for modern cooling systems.
Bubbles keep rising in the funnel because the system is open. The radiator cap holds pressure because the pressure raises the boiling point. If you're running the engine for 40 minutes without a radiator cap you're very likely creating those bubbles.
Let it cool down, fill it only as described (by opening the bleed valve) and don't start the engine until you've reinstalled the radiator cap.
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