I just started having the same problem too. I deleted my .thunderbird folder/profile and re setup my mail and the problem persists. I can view all the folders if I go into account settings, server settings, advanced, uncheck "Shown only subscribed folders". However, with that checked, if I right click on the account and choose subscribe, I am presented with the full accurate list of folders on the account. Selecting folders (such as "Sent Items") and choosing "Subscribe" checks the box. When I click OK the dialog disappears but the folder is not shown. Some times restarting Thunderbird I will see folders for the most brief of moments before they disappear again. This was a huge problem as my "Sent Items" (which I need to keep for documentation purposes) was not getting properly persisted on the server (it wasn't until I noticed the folders were gone that I caught it.) Only two folders that show (when "Shown only subscribed folders" is checked) are "Inbox" and "Trash".