Notifications for Messages keep turning back on in Yosemite
Solution 1:
The above step 4 has run together and lost its formatting. You need to run it like this:
Copy and paste each line of these commands into the Terminal window, in order. Press return after each line. IN ADDITION, IN LINE 1 BELOW, YOU MUST ADD BACKQUOTES (`) (like ', but in reverse) BEFORE "getconf" and after "DARWIN_USER_DIR", so after "cd" it reads "backquote" getconf DARWIN_USER_DIR "backquote". The backquote is edited out of the lines here due to a rendering bug in the stackexchange comment system.
cd
getconf DARWIN_USER_DIR
rm -rf com.apple.notificationcenter
killall usernoted; killall NotificationCenter