Duplicate Windows Installation: A challenge for you lot!

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Hi there!
I've had many on-going problems with my computer that started with a nasty trojan. Not being able to get rid of it, we reformatted the computer, and reinstalled windows. Various things happened, and the same had to be done again... and again. In total, Windows has been installed four times on my computer. As a result, I have recently discovered that I have four Windows folders in my C drive. They are entitled: "WINDOWS", "WINDOWS.0", "WINDOWS.1" and "WINDOWS.2". I'm not so good with the technical stuff inside the Windows folder, but the "WINDOWS" folder and "WINDOWS.1" folders are almost identical, with the same subfolders within them (eg "addins", "AppPatch", "Config"..... "system32", "temp", "twain_32"...). "WINDOWS.1" however has more files in it.
"WINDOWS.0" has no files in it, only folders with files in them. It does however have more of these files than the two previously mentioned Windows folders. Just to clarify this confusing ramble, the "WINDOWS" and "WINDOWS.1" have files like "twain.dll" and random configuration settings files in them. (They both have roughly 10 files in them.)
"WINDOWS.2" however has loads of files in it. It has many folders whose names are in blue, and start with "$NtUninstallKB" followed by several numbers. (I would be grateful if someone could explain what those files are and what they do- they seem like traces of uninstalled programs to me).
Anyway, the "WINDOWS.2" folder also has the typical "system32" folder, and such, along with many more random files in it, the last few being "WindowsUpdate.txt", "winhelp.exe", "winhlp32.exe", "wmsetup.txt", "wmsetup10.txt", "WMSysPr9.prx" and "Zapotec.bmp".

I have browsed many sites for help with the multiple windows installation problem which seems to be baffling a number of people countable on one hand, none of whom have more than one extra installation. Most people say to delete one of the Windows folders, but I have four, and they're all slightly different, so I don't know which to delete, if any.

PS: I get an error message which tells me that I WILL shut down in 60 seconds. It's initialted by NT AUTHORITY/SYSTEM, and is triggered by WINDOWS.2/system32/services.exe, with status code 1073741674. Posted this incase it was proof that WINDOWS.2 is the folder I shouldn't delete, or maybe proof that it's the one i should delete.

Please help! It's driving me loco! Confused

Hi friend
The answer to u r question is
1. u have to know first thet which is u r original Windows folder. for that click start-> click RUN-> type " %systemroot% " with out qouts. u r original windows directory will open in explorer window. Note u r Original windows folder and delete remaining all.

2. For remoel of Trojan i will advice to use NORTON Antivirus.
3. U should after deleting extra win dirs, give windws setup again from inside (Running windows) from your desktop ( Start computer -> logon to desk top-> insert Windows CD-> start windows setup-> chose upgrade-> and complete u r setup. I hope from GOD taht all u r problems will vanish. And last thing my friend Please reply me in my mail accout about my tips (Did it solved u r problem). i am waiting for u r reply. My mail address is ziaulhassanqadri.TakeThisOut@yahoo.com