I have a similar problem with a nvidia motherboard.
Has any found the reason for the issue?
I disagree that it is the motherboard. What logic to say its the motherboard was used? Did anyone troubleshoot all the other things it could be then finally conclude its the motherboard? Let me know if you already went through some troubleshooint steps.
When you hit the shutdown button windows goes through all the programs that are open and shuts them down one at a time. So what if one of those programs is corrupt and it won't shut down properly..then your computer will not shut down properly...so lets check applications first.
Click on start>control panel>Administrative ToolsL>Computer Management>Event Viewer>Applications. Now look down the list and see if you an a program that looks like it was not working right..they should all say "information" or "warning" or something else with may a red x...look at the warning and "RED X" carefully..maybe start your computer and start those programs then try to shut down and see if those are haning up and not shuttig down properly...continue checking programs until you are satisfied you they are all working correctly..let me know what you find out.