By chance I just happened to discover what it was, so I think I’ll leave this here as it might help someone in the future.
Some web pages, including an answer to this question suggest using the following code to prevent wpautop from running until after the shortcodes. Now I wasn’t able to fully understand this code, but I had it in my functions.php and for whatever the reason it was the cause of the above.
remove_filter( 'the_content', 'wpautop' );
add_filter( 'the_content', 'wpautop' , 12);