It’s quite likely that the virus itself is not in the My Documents folder. Try finding a virus scanner which allows you to exclude certain folders (I believe most do) and not scan the My Documents folder (do this in safe mode with as many unnecessary services as possible turned off of course). It might be helpful to go into safe mode with networking and use an online scanner like Panda’s. It likely won’t get rid of the problem but will allow you to pinpoint it. After that, search up on the virus and find as many associated files as possible (usually just two or three). Then go into a command prompt which is independent of windows (you can use recovery console which can be installed from the Windows CD, I don’t remember exactly how, but I’m sure you can Google the instructions) and get rid of the files associated with the virus (!!make sure you’re not deleting any important files, most viruses name themselves something very close essential Windows files; make sure you’ve got the right ones!!). Do this in the command prompt because services which allow viruses to replicate won’t be on at that time. Also, if any of the files are .bat’s or .dll’s you might be able to type “edit *.*” (* being the file name) and find out which registry keys it adds or edits (probably not though). After this, go back into safe mode, turn as many services as possible and run a virus scan again.
Hopefully this helps you