Today, I got the subdomain working by it self. I guess some of the changes I did yesterday propagated, the only thing I can think off is adding all created three SSL certificates to my https.conf site.
One problem remains.
I still can go to Apache initial page when I type https://www.domain.com, but can go to site domain.com and every thing work correctly. so I need to make https://www.domain.com point to domain.com. or fix the www some how.
Please let me know your thoughts. .. Thanks All