It's actually possible that a program that you installed didn't completely remove some things when it was done.
Might sound a bit strange... but there are some PCs that if a program was installed, for some reason the shutdown/log off took over a minute. A new program was installed, and the shutdown/log off took under 15 seconds. Like an installer glitch with things.
Actually, it could be the anti-virus or firewall that isn't closing down and causing the problems. Many windows PCs that I've seen can run up to 10x quicker if they don't have virus protection on them.
You could just bring up the task list (ctrl-alt-del) and check the number of processes... generally, with anti-virus programs/etc that the computer runs by default, there's between 40-50 processes running. Over that, and something might not of closed properly, under that, and well, you probably don't have any unnecessary programs running.
Any programs such as boink (program that shares processor usage for projects) should probably be closed prior to exiting the PC. It takes a few extra seconds to a "program isn't responding" popup sometimes. Likewise, any programs in the system tray, that you don't use, should probably be closed. Many of them just sit there and screw with the startup/shutdown of the pc.