Chkdsk is reporting 2.5 million files

I got a computer in the door yesterday with some strange problems. It is a Dell OptiPlex XE running Windows Professional 32-bit. The reported problem was a not-so-obvious virus.

   During the virus check Malwarebytes found a rootkit. It was actually one file. C:\WIndows\System32\Drivers\CDROM.SYS which I always thought was a legit file. Combofix will not run even in safe mode. It will backup the registry and simply close.

   Other oddities: Windows update will get about 3/4 of the way through installing updates and hang. Chkdsk will get to 21% of stage 2 and stop. The odd think about chkdsk is that it first reports Chkdsk is verifying files (stage 1 of 5)  2550528 (yes 2.5 million) processed.
I have never paid a ton of attention to chkdsk but there is no way there are 2.5 million files on this computer. What else is included in the number? When the computer does run is only reports a little over 100,000 files. Not 2.5 million.

   Anyway... I can't figure this one out. I have tried replacing memory and hard drive and have gotten nowhere. Has anyone seen these symptoms before?
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Test the disk using the manufacturer's diagnostic, and the RAM using memtest86+. Both are included on the UBCD:
Scott CSenior EngineerCommented:
What Windows Processional are you running?  XP, 7, 8?

If the HD checks out, I'd back up the data, do a wipe and reinstall of the OS.

That is the only way you are going to be 100% sure the machine is clean.

Your customer will be happier too as the machine will most likely run much faster.

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