You posted this question 2.5 years ago and it doesn't look like anyone responded in the forums. Did you figure out what was wrong? I'm having exactly the same problem with my G4 only it's with Leopard. It didn't start immediately after installing Leopard but now it's a big problem. The shutdown command does everything it is supposed to except just when it should click off completely the chime rings and it restarts. So I'm curious how you solved the problem with your G4 and Panther.
Wow, that was a long time ago, I certainly did work it out, eventually, I had an HP A3 printer connected to my mac and I discovered that once I disconnected it, my Mac shut down with no problems, so perhaps you also have some printer or other peripheral causing the problem, try disconnecting them and see if it works, let me know how it goes?