Kat, if you're using Windows 7, look at your bottom toolbar and see if the Windows Defender icon is down there asking you for permission to install. I recently got a new laptop that has Windows 7 and when I patched my game last night, the same thing happened to me. It appeared to stop at 99%, but then I realized that I needed to give it permission to make changes to my computer.
I've had no problems at all with the new patch. My game is running smooth as silk. <knocks on wood>