Glad you are loving your Joy! One of my spinning friends (actually it was jaykay's mum!) loved her Joy so much she found she didn't use her Traddy, even thought about selling it. She does use both now, though.
Back to the knocking...
I am confused now. In your opening post you said
one suggested it could be the bobbins so I took the spares off and, sure enough, the knocking stopped.
but now you are saying that it isn't the bobbins
Anyways, if it's
not the bobbins, here are some other thoughts.
Have you oiled all the hinges? It's the only thing they tell you you
must oil on a Joy, everything else is sealed bearings. I still put a spot of oil on the flyer shaft as I change the bobbin, mind.
Also, try placing your foot further forwards, further back, treadling more with the toes, more with the heels - ring the changes, and see if the noise changes. I found the action of the Joy quite different to the older Traddies and Travellers I'd been used to, and if you lag or beat the movement, that can cause a clack or squeak each time.