In my opinion, VirusTotal would do better to leave out obscure or second rate scanners, as they add nothing to detection, but produce a lot of false positives that confuse the user. A dozen or so major scanners are quite sufficient to find any malware without too many false alarms. I try to ignore the rest, but they still make me feel a little uncomfortable.
Some programs that defeat copy protection do so by "patching" the in-memory executable image. This is a heuristics trigger, since the exe image is being modified from outside its' code segment / code context. Some people say "it's fine, it's a keygen / patcher". But there's a secondary risk: The possibility of a secondary infector / virus package inside the patch / keygen. We've seen that happen here with the Windows Loader, as well as on public download sites who offer a "secure download" through their downloader. You always must be vigilant. Check your sources, get a SHA signature on the file from the original programmer(s) and check it against your file(s).