Same here. Plenty of things could be the cause. I'll blame the app.
Here's the thing: if you want to get the audio in sync again, FFWD or REW one click, and then quickly hit play. It might take a second or two to start playing, but the A/V should be in sync again - I'll take a manual remote action and a few seconds wait over off-sync audio any day.
And... the goofy part is that it will usually stay that in sync until the next commercial break... it always seems to lose sync during the silent "will be back soon" screen before coming back to the live action.
I've never had good luck with the ATV client. I usually end up streaming from my iPad and watching it on the ATV via AirPlay instead.