If you are running Firefox you can grab "NoScript" add-on which allows you to choose which websites use scripting. This add-on will let you see what website are being accessed by Firefox. If you are able to find out which url the "malicious site" is then we may be able to pinpoint which malware is affecting your pc.
Something else you could try is grabbing "hijack this" at
http://free.antivirus.com/hijackthis/ and letting it run a scan on your PC. It may show you what is being loaded up at boot time that might be erroneous.