I assume that there is a difference in how the project is created, because Visual Studio does not start MSBuild, since it rather hosts the assembly mechanism itself. This was answered here .
However, I had a similar problem.
In my case, the project referred to an external library, which was placed in the child directory of the project, unfortunately called "packages".
After starting MSBuild, the contents of the folder were deleted, presumably to load Nuget again.
The obvious solution was to rename the folder, and it worked.
deafnull
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