subprocess.run([program,'-force-gfx-jobs native -token='+PHPSESSID+ ' -config={"BackendURL":"https://prod.app.com","Version","live"}'])
When this command is run and you took in task manager at the command line values passed to the program the double quotes are prefixed by backslashes like this
subprocess.run([program,'-force-gfx-jobs native -token='+PHPSESSID+ ' -config={\"BackendURL\":\"https://prod.app.com\",\"Version\",\"live\"}'])