I am having a problem with Windows hanging up at the shutdown screen after it has saved settings and is in the "Shutting Down" mode. Additionally the system seems to not want to start some programs when I launch them or freezes while they are loading or running. It is not consistent as to which programs. When I check the processes list from Task Manager I see the process running for the software launched but no software on the screen.

I have run Reg edit through PC Tools, scanned for viruses and spyware, as well as done a chkdsk. I am stumped. Any suggestions would be appreciated.

Try booting to your XP CD and running the Repair option.

You want to shutting down, right?
Leave the computer, the "shutdown" screen will stay about several minutes.
Then, your computer totally off.