Check Options->Folder Preferences->Show only subscribed folders.
Try subscribing to those folders. Click "Folders" choose you folder(s), you can do multi-select, and click "Subscribe."
If this does not work it may be because SquirrelMail is configured for the wrong type of IMAP server, or does not support your IMAP server.
If the folders were not even listed, it is quite possible that they were stored on your local machine. Fire up your old mail reader and move the folders back onto the IMAP server.
Admins, please note that if your IMAP server is not listed that does NOT mean that it won't work. It just means that there are no "special" options (a.k.a. work-arounds) for your particular server.