So - After getting the bike fixed I'd left it mainly garaged for about 4 months, taking it out maybe once a month for a decent ride. The noise is back though. And it's bad.

My local garage being a yam dealer (and after contacting Yamaha), replaced the nut and washer and re-torqued to the settings outlined in the workshop manual (something like 85nm). I know others re-torque tighter around 120nm.

I'm gonna take off the cover again and see if it's worked loose. The only other thing I can think is damage was caused when it was loose before, or the threads themselves have stretched?!

Will post more once the covers back off.