Notifications for Messages keep turning back on in Yosemite
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 &quot;getconf&quot; and after &quot;DARWIN_USER_DIR&quot;, so after &quot;cd&quot; it reads &quot;backquote&quot; getconf DARWIN_USER_DIR &quot;backquote&quot;.  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