Thanks, Michael, I was getting really frustrated. I created the child theme using instructions on another site which were based on twentytwelve. Once I got the hang of it, I did the category.php, tag.php, etc files, but before then (for index and single) I’d copied the given code directly. Completely forgot about this and could not see where I was going wrong for the life of me!
Thank you. Learning on the job is fun but very irritating sometimes! I’ve now tidied up all the pages so they have the same divs and structure based on the original site code.