Since Caijoru can be in someone's dream and control Ted at the same time, that probably means Jeffrey getting scratched in the reject route wasn't caused by the dream, he just got scratched by Ted.
False positives happen more often than not when using virustotal, so you shouldn't be worried. I even checked the files myself, the files for the game engine are identical to other visual novels. The game engine used isn't malware either, it's an open source project that's been around for 18 years.