ESSEXBOY,
Right from the beginning I have accepted "I have combofix on my laptop and all I know Now is that I should have not used it unless instructed. " that we make mistakes, fine, I shouldn't have used the registry cleaners, I shouldn't have used the ComboFix, but that is why you are here, to help us. That is why we come here, to be helped. Not to leave from here with more problems. What on Earth were you thinking when you asked me to use that tool? You knew I had used Combofix and then used CTCleanit to get rid of it, you knew I had changed ownership, and permissions. Then everyone says you are the best and you know what you are doing, so I went ahead and went up to step 3 of the tool, but I felt great discomfort that the tool may not work, and then when I came across with the diference in chkdsk, I realized I should have not used the tool. Perhaps the tool DOES have some problem, which I am 100% sure it has. But you don't want to accept that. Try on your system, run sfc and chkdsk, and then run it from cmd prompt, and see if the number of files checked is the same. Would you actually run it if you had come across that difference in your own machine???