Thunderbird defaults to only showing subscribed folders. That's a way to manage the clutter when you have a lot of remote folders and you don't want to see all of them in the folder pane. You subscribe a folder by right-clicking on the remote Inbox, selecting "Subscribe", expanding the Inbox tree in the window, and subscribing whatever folders you want. You can configure it to show all folders by unchecking the checkmark at "Tools -> Account Settings ->Server Settings -> Advanced -> IMAP -> Show only subscribed folders".