Your settings in Notification Center in Yosemite has been disappeared after every time you reboot the machine? Good news there is a temporarily way to work around it from Apple Genius.
Step 1: Open the Library folder in your Home folder.
Step 2: In the Library folder, open the Application Support folder.
Step 3: Locate the folder named NotificationCenter. Drag this folder to the desktop.
Step 4: Next, open the Terminal application.
Copy and paste each line of these commands into the Terminal window, in order. Press return after each line:
cd `getconf DARWIN_USER_DIR`
rm -rf com.apple.notificationcenter
killall usernoted; killall NotificationCenter
Step 5: Close the Terminal app.
Step 6: Restart your computer.
However, Apple has lost its best quality assurance since iOS 7 and Mountain Lion
Reference: Dan Roesser: https://discussions.apple.com/thread/6605975