A couple of things:
1. Does the certificate for which the thumbprint comes from have a private key? Qlik Sense uses Transport Layer Security (TLS) to secure communication. TLS requires private keys attached to the certificate.
2. Sometimes the spaces between characters in the thumbprint do not get trimmed by the system. You may want to try taking the spaces out of the thumbprint.
I have the same issue. It used to work properly for me when I was on 1.01. This past weekend I upgraded to 2.01, and all of sudden the SSL certificate error came back. The interesting thing is when I rolled back to 1.01, the error disappeared, leading me to conclude that it does not have anything to do with the certificate or private key itself. Somehow, only the Qlik self-generated certificate gets pulled in, leading to the errors. I cannot delete the Qlik certificate, or the application won launch. Anyone has experience, please post.
I have the same issue, do you have a solution yet?
When I restart the QS service it looks like QS is rolling back all my modified settings according SSL and use there own self-signed CA certificatie.
It's getting me nuts.
(see my post: Qlik Sense server own domain SSL certificate not working)