The affected folders must still contain some of the OpenNTF code and their design can't have been refreshed properly. Do they have a reserved name (like drafts) or something?
Try creating a new folder. Does it have the problem? If not, copy the contents of an affected folder into it, delete the problem folder and rename the new one.
A pain I know, but a workaround if you can't work out why the folder design isn't refreshing properly.
Cheers,
Ben