When I had her manually turn it off at the power button and reboot it, the normal scandisk ran, and when she got to the desktop, I had to go to Start/RUN and type MSCONFIG.
Once there, go to the Startup tab and look for oddball items that you know don't go to items you need to have starting up.....in her case it was Reminder32 for her scanner software that she had recently reinstalled. It was hanging her shutdown because it had loaded up during the boot waiting for her to get online and register the product, which she had done years ago, but it had installed it again by default in the reinstallation.
So, go through that list, and uncheck the items you don't need, click Apply, and then click OK....it will ask you to reboot the computer, so at this point, say no, and then run your spyware program to get rid of any nasty crap that might be there without your knowing it. When it's done running, reboot the computer and see if that cleared up the problem.
When I shut my peuter down, it will not shut completely down. Mouse stays lit and screen tays on with a blue face