I'm going to guess that before the trojan, it worked fine. Afterwards, it didn't. Am I right? If so, then I'm guessing you installed some anti-malware software (AdAware, Spybot, etc.) to get rid of it. Problem is, those applications can block cookies as well.
Try disabling those apps first, and then log in and see if it works. If it does, then you know to go into those programs and turn off the cookie blocking. If it doesn't, then it's something else - like your browser's security settings or anti-virus software.
Sidenote: There's absolutely nothing dangerous about cookies folks. Don't block them. Doing so only ruins your online experience, as demonstrated here.