Obviously, first thing is to check for malware. Very often, if you get a screen telling you "Closing apps and shutting down" with a list consisting of a sole generic icon and no name underneath (just "This app is preventing shutdown"), it is a stuck background process, and is often malware if there is no name. Does anything running in the background other than malware could cause the shutdown to be halted (torrenting app, PC optimization suite)?
As far as I remember, new Windows 8 apps cannot prevent the system from shutting down; Windows 8 has a great amount of power over the execution of new XAML apps (they are suspended and exited on-the-fly), so you wouldn't have to force-close a Windows 8 app on shutdown. What I'm saying is that despite seeing a full-screen message that seems to be a Metro alert, it is simply because Microsoft harmonized system error messages and "Metro-ified" them: very likely you would have the same error under Windows 7 (with the semi-translucent "1 program still needs to close" full-screen interface). The culprit is therefore a background Win32/Win64 program.