Thank you again.
I seem to have found the problem. There's a Neighbour Discovery setting I've not seen before, on the Mikrotik router. Under the IPv6/ND Interfaces configuration there's a setting for an advertised MTU. I set that to the same as everything else, and things work again.
I've actually upped everything to 1472 again and not seen any problems so far.
Interesting that everything just worked
with my previous Cisco 1841 (IOSv15) router, with no explicitly set MTU on the IPv6 config. Makes me think that Cisco is even better than I thought. Shame I couldn't afford a faster Cisco replacement for my new fibre connection.
ETA: All that said, I've just discovered that my ISP has had some routing issues, for exactly the same time frame that I've been reconfiguring my network. It was resolved around the same time I did the above. I wonder which was the real problem... Talk about timing