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 🙁