Well are you using 3rd party tool for auto upgrade like SMS,Tivoli,AD deployment or Altiris.
Or you are using find unmanaged or migration and deployment wizard.
It might sound confusing for us because even SEP has a feature for auto upgrade but that only works if you have a previous version of SEP 11 installed it will not upgrade from SAV to SEP.
So if you say that you pushed out SEP and some migrated to SEP and some failed to install then can you please send us the install log on any of the computer that failed.Did you follow the steps in migration doc of SAV
Disable un-install pasword
Disable Scheduled Scan.
Disable Tamper protection.