As I recall, you need to set the port to use the secure port (636 unless a different port has been defined) AND set the SecureSocketLayer flag in order to get SSL, although my quick test with LDP against AD a second ago seemed to get an SSL connection when I used the SSL port but did not check the SSL checkbox.
I would recommend doing both, even if you get SSL without setting the SSL option.
What this does is encrypts all communication with SSL. It will only work if the server actually supports SSL (AD does not by default although it can be configured to fairly easily).