I think you may be adding a thumbprint from an incorrect cert. It looks like you have a GoDaddy root certificate which is fine, but this isn't a cert you would use to trust your site. It would be the cert for which the cert you received for your site from GoDaddy has a relationship with (as in it identifies and where your cert came from.)
The thumbprint you want to get would be from the certificate you received from GoDaddy that represents your site cert, not the root cert. This site cert (your cert) needs to have a private key attached to it when it is imported into Windows Cert Manager. Usually certs with private keys have an extension of .pfx. If you received a cert and a key from GoDaddy, then you need to use something like OpenSSL (Shining Light Productions - Win32 OpenSSL) to combine the cert and the key and then import it into the Cert Manager.
Note! Installing a cert is the same but different as importing. If you just double click a cert it's going to install where Windows thinks it should go. What you want to do is open up the certificate snap-in for the local machine and go to the Personal folder. Right click and go to All Tasks and choose import. Import your cert to this specific location. If after install two certs show up in this personal folder, the one WITHOUT the key is the root certificate. You can cut and paste this certificate into the Trusted Root Certificate Authorities\Certificates folder.
Now go back to the cert listed in the Personal\Certificates folder under local machine and get the thumbprint by double clicking the cert and scrolling to the bottom of the details. This is the thumbprint you want to enter into Qlik Sense.
After this, if you continue to have challenges with an https connection to the Qlik Sense server check the address you are entering into the url. It has to match the cert. For example, say your computer name is Sense but your cert is for Sense.CompanyX.com. In the address bar you have to navigate to Sense.CompanyX.com for your session to be trusted. What I've noticed is that this tends to work fine for the hub, but for whatever reason going to the qmc you have to enter with the Qlik Sense Hostname (listed under engines in the Configure section).
Hope this helps.
Thank you very much for the detail information you provided. I suspect the issue that we're experiencing more towards the URL that comes with certificate could be different from what we type in the url (We have the url registered with cloudapp.net address - because it's hosted with Microsoft Azure), while the url that we (as user) typed in is more like https://Sense.CompanyX.com/hub. I will try this out and will post what I find within the next couple days.
Thank you again,