May I butt in? I have a suggestion if you all do not mind?
On top of Cauzomb's great suggestions, I would like you to download the attached zip file when you get a chance and unzip it anywhere on your system. Then open the folder (Shutdown) and double-click on the batch file called run.bat, it will created about 5 registry files within the same folder.
These files are a backup of your current registry keys that the script will patch which should fix the problem if it is due to the common settings relating to system shutdown in Windows XP.
Note: Please leave those 5 registry backup files alone until further notice.
If it is related to a background system service/process and if you are still using it, my money is on LogMeIn. Remote control tools are known for their performance/bandwidth related drags as well as with their occasional interference with system shutdowns/restarts.
Additionally, after running the registry patch, you will have to reboot your system at least once for changes to take affect.
Even after doing so, there is no change, go ahead and double-click the shutdown shortcut I placed in the same folder to see if it helps. If it does, then it means there is indeed a background process causing the issue.
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