Notification settings aren't being retained
Fixed:

This thread on the Apple forums is the key:


Open the Library folder in your Home folder.
In the Library folder, open the Application Support folder.
Locate the folder named NotificationCenter. Drag this folder to the desktop.
Next, open the Terminal application and enter the following


.

cd `getconf DARWIN_USER_DIR`
rm -rf com.apple.notificationcenter 
killall usernoted; killall NotificationCenter



Restart your computer.


The issue is clearly to do with the NotificationCenter database. There are 3 files:


db
db-shm
db.wal


In my case db.wal was a 0 byte file compared with 1.9MB on a correctly working Yosemite install. Permissions were correctly set, but looks as if Yosemite wasn't writing to it. Only deleting db.wal didn't fix the problem - another 0 byte file was created on restart. Deleting everything works though!