I have absolutely no idea how my Minecraft/Web server got a virus. But, all I know is that I uninstalled Microsoft Security Essentials and installed Malwabytes Anti-Malware (passive protection, not real-time), and Comodo Firewall.
This means that while I am running without any real-time protection, the virus won't be able to even arrive the way I've set up the Firewall. Getting it to work with my Minecraft Server and FOlding@Home took a while but all in all it's OK