HTTPS Comodo Certificate - Google says self-signed

This is regarding my website and I changed from http to https a couple of days back.

I bought a Comodo certificate and configured it. Yesterday, I got a mail from Googe (Search Console) saying that, “Google has detected that the SSL/TLS certificate used on website is self-signed, which means that it was issued by your server rather than by a Certificate Authority. …”

I am sure that, it is not a selfsigned certificate. I ran a test on SSLLabs and found that there are two certificates. The Certificate #2 being issued by and a self-signed certificate. I understand that this certificate is shown when connecting with clients without SNI support.

Have I done anything wrong with the configuration? What should I do now, so that Google-bots do not complain, please help.

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