I’ve downloaded the 14.13.1 (release) branch from GitHub and have the same behavior.
When I look at the logs it appears that the first Build Solution and Rebuild Solution always fails to build the automation assemblies, but a second (and subsequent) attempt at Build Solution successfully builds the automation assemblies.
First Build Solution / Every Rebuild Solution:
47>CSC : error CS0006: Metadata file '~PATHTOUNREAL~\Engine\Binaries\DotNET\AutomationScripts\AutomationScripts.Automation.dll' could not be found
46>CSC : error CS0006: Metadata file '~PATHTOUNREAL~\Engine\Binaries\DotNET\AutomationScripts\AutomationScripts.Automation.dll' could not be found
11> Creating makefile for ShaderCompileWorker (no existing makefile)
11> Performing full C++ include scan (no include cache file)
48>CSC : error CS0006: Metadata file '~PATHTOUNREAL~\Engine\Binaries\DotNET\AutomationScripts\Android\Android.Automation.dll' could not be found
48>CSC : error CS0006: Metadata file '~PATHTOUNREAL~\Engine\Binaries\DotNET\AutomationScripts\AutomationScripts.Automation.dll' could not be found
48>CSC : error CS0006: Metadata file '~PATHTOUNREAL~\Engine\Binaries\DotNET\AutomationScripts\HTML5\HTML5.Automation.dll' could not be found
—continued—