it helps some times It seems the problem was a combination of how the msi installer was build and the restrictions windows server has towards interactive processes. I ended up using psexec to bypass this problem.
seems to work fine WorkingDirectory isn't the path where the .exe is located, it's the path that will be used as the "current" directory for the application once it starts. By default, it's the same folder as the folder where the .exe is located. For example, when you open a console window to your project folder and execute a command like msbuild, the working directory is your project folder while the executable's path is always somewhere in the .NET SDK.