Same conditions as last time except I was actually running Windows Defender at the time, doing a quick scan preparatory to a cleaning and making an image backup. Windows defender alerted both that it found a Trojan and that it had generated an error. The error code was 0x8050800c. It still finished its scan and when I looked it had system ninja in quarantine.
This time I can confirm I downloaded System Ninja from the official source, and that it was the latest version. This time I wasn’t using any cleaner, I was just launching some programs, System Ninja and Microsoft’s Disk Cleanup being two of them.
I should probably mention that I use PrimoCache. If I had to guess I’d say that this is more or less user error on my part as Windows can’t deal with what I’m loading into memory all at once, and that some of those programs have administrative privileges.
Thank you to all the other posters as it helps me in seeing this is just a rare Windows bug. I’m posting my recent experience, and the error code, so as to help the developers of this great program.