Trying to fix an infected copy of Windows from within Windows, even in Safe mode, is like trying to do a valve job on an engine while it's running. Modern Trojans, viruses, and rootkits are DESIGNED to be unremoveable by hiding themselves from Windows and the tools that we use to remove them--but we have the technology... it's called a "live" anti-virus CD. The gist of it is that they boot into Linux to run a virus scan on your Windows installation from OUTSIDE Windows, so the nasties CAN'T hide.
There are several live anti-virus CDs available, most are free. The one I use the most is from Avira, the "Avira Rescue System CD":
This is a CD image than can be used to create a CD using any standard CD-burning program, such as Nero, RecordNow, ImgBurn, Roxio, etc. (ImgBurn is free, and VERY good). AVG and Kaspersky also make similar discs, but I prefer the Avira CD, since it's updated as often as three times a day on weekdays.
(for the burning software)
A couple of tips after booting the Avira CD: click on the British flag button to get the English labels, then click the "Configuration" button to be able to select the third option, which will attempt to heal the infected files and then also select the option to rename them if they cannot be healed--the default option will find the bad files, but do nothing about them.
After the cleanup with the Avira CD, download, install, update, and run the free "Malwarebytes Anti-Malware":
After a reboot, clear the remaining malware crap out of the Windows Registry with "Comodo System-Cleaner":
My article on this: "Cleanup on Drive C, Track 56"
In general, the best long-term anti-virus solution is a virus-free image backup of your Windows installation. I'm in the process of writing an article that will address this process (it's nearly done). It will be called "Data Management in the Terabyte Age"--I will post it to my blog when it's done: