Stuart,
I have seen SmartList security get lost / reset when coming from version 9. I would suggest taking a user and assigning them to the Power User role to see if the SmartLists are available. If so, you would need to go through the security tasks and roles to make sure all users have the appropriate SmartLists. If not, you may have had an issue with the SmartList table and will need to reupdate or migrate the data from those tables.