- that sound which plays during the THL boot animation (well, who cares and I believe GravityMod2 disables it, too) and
- the notification sound for the built-in clock's timer function.
There is no menu to adjust setting for the timer function (but there is for the alarm).
These sounds stopped playing on 28th June, the same day I upgraded GravityBox from 1.3.2 to 1.4.1. And the issue persists through today's change from 20130506 stock ROM to GravityMod2 3.0 (this change included a factory reset). Could this issue possibly be GravityBox related?
Reverting to an earlier backup (GravityMod2 2.6 ROM) brings back the timer notification sound.