This is a file infector. This usually means there are so many infected system files it can't be fixed.
The infection propagates itself. It was downloaded in concert with, and hidden by, the rootkit.
This is a file infector virus which, given time, will infect every html and exe file on your computer, including system files. File infectors are notoriously difficult to remove, they are polymorphic and polyencrypted and it is practically impossible to remove them from your computer without causing more problems than are resolved.
The only realistic course of action that is open to you is to back up your non-executable (NO APPLICATIONS, ONLY DATA FILES) personal files and folders (using a DVD-R or CD-R), then re-format your hard drive and re-install Windows. If you have connected any external drives to your computer (USB or flash drives) then they should also be re-formatted.
The backup DVD should be scanned before it is used.
It should be clear that a Repair Install will not work; only a sequence where the drive is first completely reformatted.