Water Hammer, the noise is caused by a washer vibrating, akin to a reed in a wind instrument. The water carries the sound through the pipework and amplifies it. Not necessarily the WC, I'd be looking at the stop tap if changing the WC Ballvalve hasn't solved it, (you may even feel a fine vibration from the stop tap when the noise is occurring.) Try turning it down and see if that helps.
Thank you very much mate, I will try this when I get in from work.
Appreciated