Finally!! Got the SSL working.
Strangest thing using the cat command in wiki
http://pve.proxmox.com/wiki/HTTPSCertificateConfiguration was the causing issue.
I opened a GUI text editor, did copy/paste all certs individually into pve-ssl.pem and pve-root-ca.pem. After restarting pveproxy and pvedaemon SSL worked completely. SSL Checker could see the chain of Intermediate certs and the SPICE config started downloading again.
I know it is very odd that cat command did not work. But i do not have any explanation.
To sum it up this is what i did:
1. # cp /etc/pve/local/pve-ssl.pem /etc/pve/local/pve-ssl.pem.bak
2. # cp /etc/pve/local/pve-ssl.key /etc/pve/local/pve-ssl.key.bak
3. # cp /etc/pve/pve-root-ca.pem /etc/pve/pve-root-ca.pem.bak
4. Download certs from provider
5. On a windows pc opened 3 copies of Wordpad with blank pages. Saved one of them as pve-ssl.pem.txt, second one as pve-root-ca.pem.txt and third one pve-ssl.key.txt
6. Opened mydomain.crt, ca.crt and all 3 Intermediate certs on different WordPad
7. Copy/paste certs on pve-ssl.pem.txt in this order: mydomain.crt, Intermediate Cert #3, Intermediate Cert #2, Intermediate Cert #1
8. Copy/paste certs on pve-root-ca.pem.txt in this order: Intermediate Cert #3, Intermediate Cert #2, Intermediate Cert #1, ca.crt
9. Copy/paste server key on pve-ssl.ket.txt
10. Copy all 3 files : pve-ssl.pem.txt, pve-root-ca.pem.txt, pve-ssl.key.txt to /home/ssl
11. # cp /home/ssl/pve-ssl.pem.txt /etc/pve/local/pve-ssl.pem
12. # cp /home/ssl/pve-ssl.key.txt /etc/pve/local/pve-ssl.key
13. # cp /home/ssl/pve-root-ca.pem.txt /etc/pve/pve-root-ca.pem
14. # service pveproxy restart
15. # service pvedaemon restart.
The steps are pretty much what the wiki says, just without cat command.
Now the only problem is after clicking on downloaded SPICE config, it says Unable to connect to Graphics Server.Also the Console says Network Error. If i can access the VMs remotely with newly installed SSL, i will be back in business.