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Thanks for the responses guys. I didn't know what an isolation valve was or how to bleed the pipes, so I started off by turning down the main stop cock. This sorted out the problem. I tried turning the pressure up again and the knocking didn't come back - although there is a slight single knock as the cistern stops filling. It's MUCH better though. Thanks!
P.S I've also now found out what the isolation valve is! But if I turn that down, the refilling seems to get noisier so I've left it fully on.