Just a quick post before I forget,
I noticed this morning my Galaxy Nexus got a notification, and the sound it made was like a little bell which I had never heard before.
Turns out, after a quick check in the ‘Sounds’ menu within the settings app, that the only sound file I had was ‘Silent’.
I’m not sure how long this has been happening, I had missed 2 calls and 3 messages before I noticed, so I think it must’ve happened after I (Un)installed something or maybe it was something else; I haven’t updated my ROM/Google Apps for nearly a week, so I don’t think it was something I’ve flashed.

Anyways, a quick Google gave me nothing, mainly because Google wasn’t working at the time (yay for Optus! what excellent service). But I figured I was dealing with a permissions problem, so I fired up Rom Manager, hit ‘Fix Permissions’ (of course you could always use the same feature in Recovery), and rebooted.

From then on, no problems.

Hope this is helpful,
Derryn