I had the same problem after visiting some rogue internet website proclaiming to be selling anti-virus software.
To clean the infected harddisk, what I did was install win vista on another harddisk and attached the infected harddisk to the computer system as a secondary drive.
Then I cleaned out the infected disk after booting up with the clean harddisk. It's not possible to clean an infected disk using anti-virus/trojan software if you are also booting up with the infected disk; because when the anti-virus/trojan software asks you to reboot, the deleted virus/trojan will be restored from a recycle/backup copy or it was not possible to delete the viruses/trojans because they were programs in use, read only, hidden etc.
In order to use this method, you need to have some hardware knowledge and find out more about the virus/trojan using anti-virus/trojan scanners. In my case, the infection was evident because when I clicked on a drive icon, window explorer did not execute and I can't see the files in a drive or subdirectory.
In win explorer, I clicked on folder options and reset options to default. Also, I deleted a hidden file (desktop.inf) present in the root directory of each drive. It was back to normal booting speed when I use the cleaned harddisk as a boot disk again.
Try this method if you don't want to lose your programs/data files. Good luck.