Same problem. This is actually part of the system just like the dimming screen. The built-in maemo stuff always trumps our stuff and when you get a notification it effectively disables our audio output to play it's sound.

However, gstreamer seems to recover better than the pianobar did..with less scratchy/skipping effects.

Perhaps if I find a way to integrate into MAFW maybe I can change some of that.. but I doubt it since kmplayer has the same problem and you can set that to use osso-media player with no affect.