Hi,
I don’t think the issue will caused by the dual boot.
The issue may cause my third-party applications, you can boot the Windows Server 2003 system info Safe Mode to check whether you get the same issue.
You can also perform the further research as the following KB.
How To Troubleshoot Shutdown Problems in Windows Server 2003
http://support.microsoft.com/kb/324268/
Best Regards,
Vincent Hu