Mine got this too. Even when I'm not doing ANYTING. Got stuttered sound of incoming message when no applis were running.
I almost got fully reflashed my device (even with eMMC image reflashed) - so it can be called 'clean install'. I had no applis installed at all for about 2-3 days (yes, I was hunting for the bug, hoping if an application from somewhere outside PR1.2 is the reason) with no success - sometimes it's just enough for n900 to lay quietly for some time without running processes at all to make this noise appear suddenly with an sms etc.
I thought that CPU load is the case - so in this case overclocking and/or renicing would be a temporarily solution. But none of that solved a problem.
Yet I'm not talking about impossibility of simulatineous sound sources, such as cannot listen to the music via default player and to play Angry Birds with sound... Is it pulseaudio I know???
Or is ALSA broken?