I certainly noticed this get worse from PR1.1.1 to PR1.2 especially as I mainly use gpodder + panucci - really getting fed up of losing parts of the conversation in a podcast when an email comes in.

I've mitigated the issue somewhat by using the tweaked kernel that bumps the clock speed up to 850, but it's still not perfect. I also hear that the next release of Panucci for the N900 will renable the option to use the native audio decoder instead of it's own which is meant to be less buggy. That may help.

What I do know is that using the native media player does at least put the phone in a mode where alerts get changed to a simple background beep rather than the full alert tone set for the profile. this certainly would help panucci if it did the same.