You know, I never really considered throwing my tools into VirusTotal before. Checking it, it seems to trip a few trojan detectors and I don't know if I can do anything about that. The tool needs to write/read data else it wouldn't be able to do what it's supposed to do. If it makes you feels safer, you can run the JAR file without needing the executable by opening a console and entering the following line into it.
java -jar [JAR location]
Funnily, looking up the "detected viruses", someone had the same false positive playing Bridge Constructor: Portal a few years back.