A freshly downloaded copy of system-ninja-portable-3.1.zip will sometimes throw a .NET error, while the exact same file (confirmed by matching MD5 checksums) that has never been uploaded to the internet will run completely fine.
Download the installer version, install; go to “C:\Program Files (x86)\System Ninja” and copy everything except for the uninstaller files to a new location. Uninstall System Ninja, continue using the files as a portable program.