Thanks for the help guys after I got the automatic root certs working again in our infrastructure (It was disabled at the top of the domain policy in Active Directory) the 12.1.4100.4126 installation both installs, or upgrades, smoothly....points awarded.
James007, now maybe the servers that I spot checked the install/upgrade on already had root certs for the 12.1.4013.4013 install.... but I'm pretty sure the only SEP version that need "new" certs was 12.1.4100.4126. It's reproducible on any server that I prevent from getting new certs.
I had no problems taking a newly provisioned server and installing or upgrading 12.1.3001.165 or 12.1.4013.4013 without needing new certs...I refer to the full versions because the MR/RU/MP stuff is getting confusing....not sure if what I referenced is RTM or not ....I think so though.