Really weird occurance after reinstalling OS - can anyone help?

Guys, this is really weird and I don't know what to do. So, I'll give you the full story.

First off, here's my computer specs:
Dell XPS DXP051 (basically a Dell XPS 400 bought in late 2005)
2 GB RAM (4 separate 512 MB sticks)
Local Disk (C) 108 GB
Backup (D) 36.7 GB
Pentium(R) D CPU 3.00 GHz Processor
Windows XP Home SP2 was the original OS.

My system was relatively unstable to begin with. I had a boot sector virus (Troj/Mbroot-E) that Webroot Internet Security Essentials would not remove. I don't know why, but whenever I quarantined it, it just didn't remove. My computer was periodically freezing because of it, I guess. But other than that it would work fine for several hours at a time, so it was okay to use.

So recently I decided I was going to reinstall the operating system because of all the problems. So, I first had to remove Windows XP SP3. It was in a state of half-installation for some reason: I had SP3, as in, it showed up in Add/ Remove Programs, but it didn't detect that I had it. So, I went to Microsoft.com and tried to download the SP3 update thinking it would fix the problem. When I was installing this update, however, it froze on me halfway through and I had to do a hard shutdown by holding the power button.

I then turned on my computer. Because I was in the middle of an installation, I was missing several operating system files. The Windows XP Screen was loading, it displayed this message: "Autochk.exe missing, Skipping AUTOCHECK." So, I figured the Operating System had been screwed up by what I just did. So, I decided to boot from the XP disc to repair the OS.

I have multiple computers, and it turns out I used the wrong disc. I used a standard SP3 disc and it said I couldn't activate. So, I simply popped in an SP2 disc which I also had then installed XP from there. XP then started normally and I have all my previous files.

But now I have this very odd issue:

My computer now created copies of my hard disks. For some reason, I now have a Local Disk C, Local Disk E, Backup D, and a Backup F drive. Disks C and E contained the exact same files except C had the corrupted OS on it, and E had the new installation. Now, my OS boots from E, but all my program files are booting from C! (Such as MS Word, Photoshop, etc.)

Here's the weirdest part, though: The computer thinks that each drive still has 108 GB of space on it, and I KNOW for a fact that my computer cannot hold 216 GB worth of files. So what gives? It's not really a ghost copy, because when I delete something from C:, it stays on E:, and vice-versa.

I tried an experiment as well: I formatted the F: drive (the second Backup drive) to see what would happen. It formatted drive F: and it didn't affect anything. I am now going to remove drive F: entirely (umm, how do I do that?) But Im afraid to go any further with my main Local Disks.

What should I do? Should I copy all the files from C: over to E: except for the WINDOWS and i386 folders? Because the disks both have the same files on them except for the OS, like I said. So should I just let it overwrite what it must? But if I do that, what will happen when my PC next boots up?

My goal is to remove the corrupted operating systems and have a single, working Local Disk instead of a 'ghost' copy. It's really weird. I hope I explained enough! Please tell me if you need clarification and I thank you so much for your help.

Does anyone know what's going on here!?

 

Sure it was okay to use - NOT, now back up your data and get over to the Read & Run me in the Malware section.

 

Alright, I'll attempt to remove the boot sector viruses. In addition, after the disk duplicated itself, I now have Two boot fector viruses: Troj/Mbroot-E and Troj/Mbroot-F. Great.

Aside from that, any help with the main issue?

 

Unless I'm wrong, the boot sector virus was the main issue that was causing problems? A regular format does not overwrite the MBR, so I would recommend doing one of the two following suggestions, use your hard drive manufacturers utility or this, http://www.majorgeeks.com/Dariks_Boot_and_Nuke_d4596.html. Either utility will "0" your hard drive, overwrite the MBR thus removing the boot virus problem, and restore your hard drive to an as manufactured state as possible, minus the wear. Then you will need to reinstall the OS. Hope this helps!

 

Oh, I forgot to mention this, and I feel really dumb.
When I was in the SP2 disc mode I went into recovery console and I typed in fixmbr or whatever and it wrote a new boot sector. Does that have anything to do with anything? When I was on a website it told me to do that...Were they wrong?

 

WinObj may be able to point you in the right direction for your phantom drive problems but as you have boot sector virus issues, these may be the cause of the ghost drives, ie., misreporting to Windows.

 

Hard to say, but I would still recommend zeroing the hard drive as a sure way to certain that the virus is gone, and reinstalling the OS.

 

What if I have some files on there that I want to preserve...Zeroing it would be bad.
Also, I paid for some software like Microsoft Office and Webroot Internet Security Essentials, etc. Will it let me re-enter the same license key if I want to simply reinstall those applications once I 'zero' my hard drive?

 

Alright...Im backing up my MOST important files onto two flash drives...I thought I'd never ever do this but Im going to delete 90 GB of crap using the DBAN utility...

But don't worry. I'm reinstalling almost all of that crap. If I can remember what I had to reinstall...

 

Alright I'm finally done with this whole process...Thanks for referring me to Darik's Boot and Nuke. No longer have ANY issues with computer. Thanks a lot

 

Glad that it worked!