hi,
Which Operating system you are using? If you linux means it will take some time for close all applications,but windows means you can change some setting and increase your shut down process speed.
regards.
What kind of OS you are using? If its XP. You can try do follow:
Go into BIOS
Disable Floppy 1.44
then try reboot and see if it resolves the problem.
Also make sure you have patched the OS with all most updated updates from MS.