The basics of process and file locking in Windows... If a file is opened by a process, or the file starts the process - that said file is locked by the system, you can't do anything to it. Now, every applications out there that runs on Windows have the same behavior, be it a "legitimate" applications like Winamp, Microsoft Word, iTunes, Windows Media Player, OR an "illegal" application that harms your computer like virus or malware. With that basics covered, there's another behavior in Windows that let's one process communicates with another process, it's called InterProcess Communication (IPC). By leveraging this, a virus or malware can hinder an Antivirus or Antimalware easily, even at times can crash the said AV/AM. Now, if you really want to clean up your system, you can't have the OS running, because of the file locking behavior, you can't clean a running virus, the process locks the files... Some virus even have the ability to re-copy it's "body" if the "body" is deleted by some AV/AM.
Installing and scanning virus/malware in an infected computer is moot to some degree, you won't get a 100% clean system, because you'll never know if there's no other virus running which hinders your scan, or if your AV is not compromised by the said virus/malware. My best suggestion still stands, get the AVG Live CD (or any other AV live CD) a try, or plug your disk to another clean system and scan from there, at least it will catch something, hopefully it will catch most of your pesky virus/malware... Good luck.