I'm trying to build a deployment to roll this out to the office next month, but R2 will not install.
I downloaded the 2016 BDSP installer from the subscription site and created a deployment. At the end of the deployment creation screens I selected add updates and applied Update 1 for R2 which states it should apply R2 and all service packs. So far, so good.
Upon running the deployment Revit is installed, but the update is not and it gives the dreaded, "This service pack could not be installed because it is not designed for the version of Revit 2016 that is installed on your computer" error. The log states that the update succeeded, but it lies.
This is the update applied to the deployment:

The error message on install:

Revit installs with this build 16.0.490.0:

The install log line stating update success:
2016/1/29:10:11:30 <MyUserName> <MyComputerName> Installing : "\\<MyServerNameAndFilePath>\Autodesk_Revit_2016_R2-x64_UPD1.exe" REBOOT=ReallySuppress ADSK_SETUP_EXE=1
2016/1/29:10:19:13 <MyUserName> <MyComputerName> Install Update 1 for Autodesk® Revit® 2016 2016 Release 2 Succeeded
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Bobby C. Jones