This is a real problem and I can answer this question so it has enough specifications.
We have no idea how your system is set up and what could be running in the background
That is not necessary to solve his problem, troubleshooting stays the same no matter what computer you are running or background processes are running. The way to solve this kind of problems is to take a trace of the system, then this trace would allow you to pin-point the problem.
So, the answer to this question is that he should take a trace and inspect it. His system set-up or background processes are not going to show the culprit of his problem so asking him to specify that and closing his question is not going to help him in any way...
Could you help reopen this shutdown question?