I have also have an intermittent problem of not shutting down. Currently it is shutting down but every so often it will act up.
Quick guess, some process is still running and the system waits until that process finally quits, then, and only then, executes the final power off signal. What the process is, I haven't a clue, but I have seen this on my own machines. If one waits, and the machine does eventually shut down on it's own, the next time the wait is usually shorter, and usually by the third or forth shutdown is back to a normal shutdown, as soon as the last message in the shutdown procedure is posted. Kind of like the system is learning a better order to shut down the individual processes. The last time I saw something like this was a few years ago, on a newly built machine. Within a few days everything was shutting down smoothly and the delayed shutdowns never reoccurred. I did nothing to force the shutdown; just waited until the machine did it on it's own.
The only time I've ever had a machine completely refuse to shutdown was on a 1997 Sony, running Win95 OSR2, and still under warranty. I took it back to where I bought it, and was told all machines told you when it was time to push the button, that they didn't actually cut the power. I told them the machine had always shut down completely, on it's own, and that this was something new. That went back and forth for a while, then while messing with the settings, I found a reference to apm being turned off. I had no Idea what that meant, but turned it back on, and on shutdown the machine went through the process then powered off, in front of the tech staff. Turns out none of them had a clue what apm was, and had never seen a machine power itself off. Before I left, they were running around the store, checking the new machines, and all that had the OSR2 installed, did, in fact, do a full power off on shutdown.
I learned two things from that. Never trust the tech guys when they tell you, you don't understand how a computer works. That means they are the ones who don't understand, or they are giving you a snow job so they can charge big bucks for a simple setting change, once you leave the machine with them. That leads directly to lesson two; know your own machine. If one takes the time to learn how ones own machine functions, one is never at the mercy of the stores "highly trained technical staff." Most seem trained to only take your money. Think Geek Squad, and I rest my case.