Some functionality within Civil 3D 2016 might be missing after deploying the software through or other deployment tools.
Following script could help to fix this issue for all the users logging into the machine after deploying the software as System account.
Please use this script to deploy through SCCM instead of the single setup.exe command line.
REM Take Backup of the existing xml file
IF EXIST C:\ProgramData\Autodesk\appIndex.xml (REN "C:\ProgramData\Autodesk\appIndex.xml" "appIndex.ORG")
REM Install software
Start /w .\Img\Setup.exe /q /w /I .\Img\c3d2016x64.ini /language en-us
REM Delete newly created XML file
Del /q "C:\ProgramData\Autodesk\appIndex.xml"
REM copy backup xml file
IF EXIST C:\ProgramData\Autodesk\appIndex.ORG (REN "C:\ProgramData\Autodesk\appIndex.ORG" "appIndex.xml")
REM Copy Missing C3D_Profiles folder from the deployment image
xcopy .\Img\Content\en\C3D_Profiles "C:\Program Files\Autodesk\AutoCAD 2016\C3D\en-US\ContentPacks\en\C3D_Profiles\"