There are some very difficult viruses lately that require a reboot to get deleted BUT.... unlike others that can be killed at reboot, they duplicate themselves before you even know it, (most propably everytime you press the start button) and at the same time also hide themselves, change name etc...
Sorry to brake you the bad news but NONE of the known Antivirus software can do anything about them -at least for the moment. 100 reboots, 100 virus scans, and each time you get another new virus!! The only way to clean your machine is boot from another hard disk, and use the antivirus software from that 2nd disc. It's always a good idea to have 2 hard discs anyway, they can save you from lots of problems.