Thanks everyone. I came across these YouTube videos of exactly the same thing and these seems to suggest the same about the grease and the bolts, so here's hoping...
Update: So a gas engineer came out from a different company and I explained the issue and told him what I thought the issue was based on the videos and advice given by ianmcd.
He started by loosening the nuts slightly which seems to have solved the problem. He could see that grease had been used correctly on them.
I'm now on edge all the time waiting for the noise to start again, ha ha.
I've removed my original video referenced earlier in this thread, as the other YouTube videos upthread show the problem much better.
And to clarify for anyone coming across this thread in the future. I initially thought the noise was coming from the top of the boiler/flue outlet, but it wasnt.
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