If not malware most likley driver issues. At any rate....do you know when it was working and shutting down properly? Can you system restore to that time? Here is an another answer which I googled for you:
The wireless mouse/keyboard drivers could be causing the issue, but see
> general shutdown troubleshooting below for more.
>
> *****
> Shutdown issues are generally caused by a program and/or process that is
> refusing to exit gracefully. The program and/or process can be from
> malware or can be legitimate (such as an invasive antivirus like Norton or
> McAfee). If you are using a Norton or McAfee product, uninstall it and
> replace with a better program such as NOD32, Kasperksy, or Avast (free).
> The Windows Firewall is adequate for most people. With Vista, shutdown
> issues can also be caused by old/poorly written drivers so make sure all
> drivers are updated. See Step B. below for general driver directions.
>
> A.The first step is always to make sure your computer is virus/malware
> free.
>
> http://www.elephantboycomputers.com/...moving_Malware
>
> B. Drivers - The First Law of Driver Updates is "if it ain't broke, don't
> fix it". Normally if everything is working you want to leave things as
> they are. The exception is that heavy-duty gamers will usually want to
> update their video and sound drivers to squeeze every last bit of
> performance out of the hardware to get the fastest frame rates. If you're
> not one of those people, you don't need to update your drivers if there
> are no problems you are trying to solve.
>
> Never get drivers from Windows Update. Get them from:
>
> 1. The device mftr.'s website; OR
> 2. The motherboard mftr.'s website if hardware is onboard; OR
> 3. The OEM's website for your specific machine if you have an OEM computer
> (HP, Dell, Sony, etc.).
>
> Read the installation instructions on the website where you get the
> drivers.
>
> To find out what hardware is in your computer:
>
> 1. Read any documentation you got when you bought the computer.
> 2. If the computer is OEM, go to the OEM's website for your specific model
> machine and look at the specs (you'll be there to get the drivers anyway)
> 3. Download, install and run a free system inventory program like Belarc
> Advisor or System Information for Windows.
>
> http://www.belarc.com/free_download.html - Belarc Advisor
> http://www.gtopala.com/ - System Information for Windows
>
> C. If the computer is virus/malware-free, drivers are current, and no
> Norton or McAfee programs are installed, then do clean-boot
> troubleshooting to see which program/process is the culprit:
>
> How to perform a clean boot in Vista and XP -
> http://support.microsoft.com/kb/331796
>
> D. If you need more information, here is an excellent shutdown
> troubleshooter:
>
> http://www.aumha.org/win5/a/shtdwnxp.htm
>
> Standard caveat: If troubleshooting the issue is too difficult - and there
> is absolutely no shame in admitting this isn't your cup of tea - take the
> machine to a computer repair shop. This will not be your local
> BigComputerStore/GeekSquad type of place. Get recommendations from family,
> friends, colleagues.
> *****
>
> Malke
> --
> Elephant Boy Computers
> www.elephantboycomputers.com
> "Don't Panic!"
> MS-MVP Windows - Shell/User
>