Comment 2 for bug 437429

Sound theme sets one of the four alert sounds (bask, drip, glass or sonar). It does not change the system-ready sound.
One of the many workarounds to your wish is to go to (with root priviledge) the directory /usr/share/sounds/ubuntu/stereo and change the name of the file "dialog-question", for example to "dialog-question-backup".
Now the system-ready (drums) sound does play no more.