I don't have enough reputation to comment so I copy / paste my answer here since this question has more views.
I had a similar issue during QGis 2.18.10 startup.
SSL Certificate Errors occured accessing URL :
https://ubuntu.qgis.org/version.txt
Unable To Get Local Issuer Certificate: The issuer certificate of a locally looked up certificate could not be found
I fixed it by going to https://ubuntu.qgis.org/version.txt with IE.
Alternatively, using Powershell :
Invoke-WebRequest https://ubuntu.qgis.org/version.txt
or (for Powershell < 3.0)
(New-Object System.Net.WebClient).DownloadString("https://ubuntu.qgis.org/version.txt")
My guess is that any of these actions add the qgis certificate (or maybe let's encrypt CA) to the certificate store.
Save SSL server exception