|The message appears sometime after you click the shut down button if your PC has been running for a long period of time. Usually the ATi or Nvidia graphics controller is still in use and needsd time to properly close if you had been previously playing games for a long period of time or running a program or software that is extensive in use like video editing/compiling.|
If you click End Now, it will forcibnly shut down the drivers or app still using resources. It's much like an external HDD that will not eject from the usb because the spin down of ther platter is still operating and last minute little details are still being sent to or from the external hdd or other device. The same applies to drivers and programs. Best to Cancel the shut down and allow a few minutes before shutting down. Always shut down with all apps closed.
The End Now option doesn't really corrupt the hdd or operating system, it just forces any app still running to cut short its procedure. However, sometimes an End Now still doesn't shut down and if you have to do a Hard Shut Down, it is advisable to reboot to desktop then shut down safely.