updating the bios was a mistake. the bios may be caved now.
Try going in the programs and delete service pack 3. This theoretically should return it to SP2.
start>control panel>add remove programs>look on the list for SP3>right click on SP3>left click delete.
it takes a while...also doing a repair install will return the OS to the default state. The directions are posted in this forum sixth post from the top. It does not erase your personal files, but reloads all the windows defaults, including the OS drivers...
But I cannot say if failure to shut down is caused by a corrupted OS or damaged bios.
There is noting to be gained from deleting (or even properly uninstalling) SP3 because without it, you won't receive critical security updates every time Microsoft's package is hacked. With SP3 you get that support until the year 2014. A Repair install is not a good idea either.
Before trying a Shut Down, press Control Shift and Escape together and look in the Task Manager>Applications tab to see what's running. If nothing is, click on Processes and double click the header of the CPU column to bring the highest resource user to the top of the list, right click it and click to End Process.
You may have to repeat this process a few times to nail the guilty party.