seeing a similar issue with accounts transferred in from cpanel and accounts that where natively created on this server ... did sandeep ever confirm the message,...
in my case the dns for the zone i'm attempting to put the ssl on IS the server I'm on, I have A records for both @ and www
have also tried it with an A for @ and CNAME for www, loosing way to much time attempting to migrate about 130 sites but looking at whm and cloud linux being the solution just hate to go that route when I spent the time selling this to the higher ups.