This is a ClickOnce build. It works fine for .NET 4.5.1. 
.NET 4.6.1 SDK is installed.
MS Visual Studio 2015 Update 2 installed.
Windows 7 is the OS.

The GenericBootstrapper is: "HKEY\_LOCAL\_MACHINE\SOFTWARE\Wow6432Node\Microsoft\GenericBootstrapper" with a 12.0 and 14.0 also.

* In the project files I changed the ToolsVersion from 12.0 to 14.0.
* I changed the TargetFrameworkVersion to 4.6.1.
* And the bootstrapper to:

> 
> 
> ```
> <BootstrapperPackage Include="Microsoft.Net.Framework.4.6.1">
>   <Visible>False</Visible>
>   <ProductName>Microsoft .NET Framework 4.6.1 (x86 and x64)</ProductName>
>   <Install>true</Install>
> </BootstrapperPackage>
> 
> ```
> 
> 

Here's a warning from the log:

> 
> C:\windows\Microsoft.NET\Framework64\v4.0.30319\Microsoft.Common.targets(4513,5):
>  warning MSB3155: Item 'Microsoft.Net.Framework.4.6.1' could not be
>  located in 'C:\tm1\HE\HE.Manager'.
>  [C:\tm1\HE\HE.Manager\HE.Managercopy.csproj]
> 
> 
> 

Here's the error log:

> 
> C:\windows\Microsoft.NET\Framework64\v4.0.30319\Microsoft.Common.targets(4513,5):
>  error MSB3147: Could not find required file 'setup.bin' in
>  'C:\tm1\HE\HE.Manager\Engine'.
>  [C:\tm1\HE\HE.Manager\HE.Managercopy.csproj]
> 
> 
> 

Why is this happening with 4.6.1? 

In our batch file here's our MSBuild call:

> 
> frameworkPath="C:\Windows\Microsoft.NET\Framework64\v4.0.30319"
> 
> 
> %frameworkPath%\msbuild %PROJECT\_NAME%copy.csproj /target:publish
>  /property:......
> 
> 
> 

This doesn't work properly with .NET 4.6.1. We get the error I mentioned in my first post.

In my registry 

> 
> "HKEY\_LOCAL\_MACHINE\SOFTWARE\Wow6432Node\Microsoft\GenericBootstrapper"
> 
> 
> 

if I add a 4.0 item with a path "C:\Program Files (x86)\Microsoft Visual Studio 14.0\SDK\Bootstrapper\" it works.

Why is it not using the registry item 

> 
> "HKEY\_LOCAL\_MACHINE\SOFTWARE\Wow6432Node\Microsoft\GenericBootstrapper\14.0"
> 
> 
> 

?

Also......

If I change the frameworkPath to...

> 
> frameworkPath="C:\Program Files (x86)\MSBuild\14.0\Bin"
> 
> 
> %frameworkPath%\msbuild %PROJECT\_NAME%copy.csproj /target:publish
>  /property:......
> 
> 
> 

and run the MSBuild call it works.

I've reinstalled the .NET 4.6.1 SDK and still no luck.