I used Spybot but even though it scanned malicious files, it doesn't detect a threat?

Virtumonde is a nasty threat, so are the other ones you named. I won't go into how weak of a security program Spybot is but It's not very good anymore. But you have nothing to worry about. Spybot wasn't scanning those files you named. It was looking for them. When you see virtumonde, that is the threat that spybot is scanning for at that time.