Just tried iOS7 with a few rips I was having trouble with and all are playing back perfectly now, about time
I've decided to try too and after the update, the files that caused the ATV to stutter, lose audio and stop playing all play fine now. Unfortunately, without a similar update for my ATV2, I've used Seas0nPass to Jailbreak it just to edit the /etc/hosts file to block updates to that and keep it at 5.3 which also works perfectly. If anyone cares to confirm whether the last 6.2 update Apple released for the ATV2 fixes this (the release notes are less than useless) I would be happy to update it but until then, JB it is.