Install Problem Drive as a slave to a known good drive with updated AntiVirus. Then scan the slave/problem drive with updated antivirus AND online scans
www.trendmicro.com and panda free scan. Then run lavasoft adaware and spysweeper to scan the problem drive. After all of that, take the problem drive and put it back as master, attempt to boot into safe mode and msconfig everything away, reboot and see if that doesnt let you function in windows.