For the new issue, add a powershell script task in your build definition to import the certification.
$pfxpath = 'pathtoees.pfx'
$password = 'password'
Add-Type -AssemblyName System.Security
$cert = New-Object System.Security.Cryptography.X509Certificates.X509Certificate2
$cert.Import($pfxpath, $password, [System.Security.Cryptography.X509Certificates.X509KeyStorageFlags]"PersistKeySet")
$store = new-object system.security.cryptography.X509Certificates.X509Store -argumentlist "MY", CurrentUser
$store.Open([System.Security.Cryptography.X509Certificates.OpenFlags]"ReadWrite")
$store.Add($cert)
$store.Close()
Refer to this question for details: Visual studio team services deploymen/buildt certificate error