Some antivirus programs are so stupid that any auto-updating program that asks for and/or gets access to the internet will be detected as a "trojan horse" especially if it isn't digitally signed. Do you have a firewall running? Windows firewall only blocks incoming connections, making it wide open for any trojan horse or any other program running on your computer to get access to a server on the web, without your permission.

It wouldn't surprise me one bit if the alerts are caused by facebook if you installed and/or play any of the games there. I strictly forbid it. I don't trust facebook apps at all if for no other reason than making your browser more vulnerable to attack, even if the apps themselves aren't malicious.