I’m having the same issue. All other inputs work fine to my Marantz NR-1501, but the ATV2 will have audio drop out in every app. I can get it back after switching around the audio souce a few (dozen?) times.
I also have a problem with audio AS WELL AS video dropping out using Media Player only (as far as I reckon). it is only for a fraction of a second but it is very annoying.
After playing music with the last.fm screensaver set to swithc on after a certain no of minutes, sometimes the AppleTV menus will show on top of the screensaver and only a reset will restore it back to normal.
These surely must be bugs ???
Never happened to me before, but only after updating to 5.2, re-jailbreaking and reinstalling aTV Flash.
I run 5.2 as well as the latest aTV Flash w/updates (as of 27.02.2013)
Also I have the same problem in the FireCore mediaplayer, so now and then the audio drops for a split-second.
But its an anoying when watching a movie or playing music. This problem did occur after i’ve updated my appleTV with the latest firmware (5.2) and installed the latest aTV Flash.
(I am owner of two appleTV 2’s and both are having the same problem)