The virus may have gone deeper and crippled Windows itself to force it to boot up with that virus loaded. I'm pretty good at manually removing viruses, but you'll need some technical knowledge with Windows.
1. Make sure you've removed that virus and remember the file path it was in.
2. Try to boot into safe mode (keep tapping F8 on bootup).
3. Check if the virus is there. You must check manually, as the anti-virus is not loaded while in safe mode, nor any other startup programs.
IF THE VIRUS IS STILL THERE:
The virus has infected the system files. Insert your Windows CD and restart the computer, booting up with the CD. I've found an okay website with instructions to repair the system files. Make sure you backup. This way may be quite a hassle.
http://www.michaelstevenstech.com/XPrepairinstall.htmIF THE VIRUS IS NOT THERE:
If you haven't already, perhaps you could try checking your startup applications and processes. Click on your Start Menu, press Run, and enter in 'msconfig'.
Look through anything suspicious in the Services and Startup tab. Be careful with disabling some of the Services though, it can stop your computer working if you uncheck the wrong ones. Although the computer will still work if you disable all the Startup items.
If that still doesn't work, you may have to check if the virus has installed any drivers. Right click on 'My Computer' and click on properties. Go to the 'Hardware' Tab, then 'Device Manager'. Look through all the hardware and see if anything is suspicious. Disable it. If that doesn't help, I'd recommend re-enabling it again.
Well, hope that can help you manually remove the virus. I just noticed how much I wrote