I had a similar issue when i was creating an application that communicated with a server over HTTPS using two-way SSL.
This was causing a delay of a full minute when the initial request was made
It ran in WinPE where hand clicking through the local group policy editor was not an option.
There also is no way I am aware of to register a root authority in this environment and it is running in an incredibly restricted environment so it can not access windows update (not that it would find our corporate CA there anyway).
The registry value you are looking for is
HKLM\Software\Policies\Microsoft\SystemCertificates\AuthRoot
DWORD DisableRootAutoUpdate = 1
Source: http://www.group-policy.com/ref/policy/452/Turn_off_Automatic_Root_Certificates_Update