It looks like several things were missing after the MT upgrade and now I have fixed the archives. Basically the archive templates were missing for some reason, but fortunately I had archive templates in a test blog. So I switched to the test blog, went to Design then templates then archive templates. I then selected the code for the category archive, went to the same location in the live blog and pasted the code into it. After saving the code I created an archive mapping that pointed to category/sub-category/index.php and then rebuilt all of the category archives – it then worked. Unfortunately I’ve just realised that the template links back to the atom.xml file and not feedburner so I have to republish again – I’ll be doing that tonight 🙁
Thanks to a tip off in the comments, I’ve fixed my RSS feed. When I moved from the old version of MovableType the index.rdf file didn’t get regenerated as before but instead the atom and rss feed got generated instead – unfortunately my feed at feedburner didn’t know that! I’ve since changed the feed at feedburner to use the atom feed AND updated the meta tags in the template to point to the feedburner site.