When I upload my protected file on virustotal.com, I get a false positive from one of the listed antivirus

Some (not widely known) antivirus, have a very bad heuristic and they even report as virus any application with a slightly different PE header. They don't even look at the code inside the application. They also ignore any file that is digitally signed and report it as virus.

You can use the Stealth Mode insertion to hide your protected (virtualized) code from those antivirus. In any case, most antivirus have a link where you can upload the protected application, so they will white-list it.