So perhaps you have used a web-interface to create new subfolders on an IMAP server. The problem is that thunderbird doesn’t show them, and no amount of clicking on things seems to solve the problem or show these subfolders.
The answer is to click on the account in question (i.e. one level up from your Inbox), then click “Manage Folder Subscriptions”. From there on it should be obvious – find the folders, and tick the boxes. Job done.