Hi Jaskarn,
I had a similar problem and I fixed it by going back to the Legacy WebUI. Indeed, in the new one, the certificate does not show.
So solution is :
--go to your FreeNAS WebUI
--switch to Legacy
--set the certificate there
Once done, the new WebUI may not even show the certificate in use, but it will be used and you will be able to reach your FreeNAS over SSL.
Good luck,