I have the same problem from june. Since then, when I try to install an SSL certificate, the domain dropdown remains empty and the message "DNS of your domain doesn't point to this server or you have htaccess restrictions" appears.
I'm 100% sure that the DNS are good and no .htaccess file is bothering.
I've rebuilding the new webserver with php-fpm (actually version 0.9.8.745), but still no work.
Every else on the server works perfect, just the certificates problem.
A strange thing is that I can renew the certificates for the domains that I have already added, and works perfect.