There's a good chance that this is happening because the server is presenting a certificate that's different from the one you expect. You can connect and download the presented certificate by using the method SSLFTPClient.getServerCertificate(String,int,boolean). This method returns an SSLFTPCertificate object, which you can then write to a PEM file using the SSLFTPClient.writePEM() method. Once you have the certificate, try comparing it with the one you're currently using and also try connecting using that certificate.
-Hans (EnterpriseDT)