could be that some application is "reluctant" to quit. Or maybe it just needs to process something and that's taking a while. OS X won't shut down or restart while an application is open - they all have to quit first.
Found that one out when I had Photoshop (Classic one) open and tried to restart - I had been editing a document in Photoshop and hadn't saved it. The save dialog came up, but I had gone to make myself something to eat while my computer was restarting. When I got back, OS X had given me a dialog that said something like "Restart timed out because an application refused to quit" (it was something like that. I think it may have even named Photoshop - which would be something, 'cause it was running in Classic).
So it's very possible some application is just taking a while to quit.