If I have the following lines in winnt.sif:

[Proxy]
    Proxy_Enable=1
    Use_Same_Proxy=1
    HTTP_Proxy_Server=myproxy:80
    Proxy_Override=<local>

Then the PC cannot contact my SUS server. If I remove those lines and enter the same information by hand in IE Internet Options, Lan Settings it all works. What is different about doing it in winnt.sif besides the fact it is going into the default user profile?

[Branding]
BrandIEUsingUnattended=Yes

Do you have this ?

Yes

Changing this to No and rebuilding gets SUS working but windowsupdate.microsoft.com still fails and I obviously don't get the proxy settings and homepage added in.