Audio out of sync with optical out

Hi,
I've connected audio from ATV 2 times to my receiver. My Sony television has an optical out connection so it can act as a passthru for audio to my receiver. However, it's always stereo, I can't get surround from it. Apple says it sends the same audio over HDMI and optical out. So I connected ATV directly to my receiver with the optical output. Result: I do have surround now. So I guess my Sony is at fault for not passing along surround.
This is my setup:
1) ATV -> HDMI -> Sony LCD -> optical out -> receiver
2) ATV -> optical out -> receiver
My problem:
Setup 1) gives me no surround but audio and video are synced perfectly.
Setup 2) does give me surround, but audio and video are OUT of sync.
My video is generated by Handbrake 0.9.3 and contains both AAC stereo and AC3 surround passthru.
It's strange, because if you have this audio delay problem you would think it's caused by the television because that's an extra device sitting between source and receiver.
Any ideas what is causing this problem? Is Handbrake not able to add AC3 correctly or is ATV playing sound in sync over HDMI but not in sync over optical out?
Thanks,
Jef

Thinking about this a bit more, I think I could have an idea as to what the problem is - the AppleTV firmware. I believe that there is a timing difference between HDMI and the optical audio output. Let me explain...
My AppleTV is hooked up using HDMI for video only (direct to my TV) and the optical is hooked up directly to my audio receiver. Since there is no setting in the AppleTV menu to choose the output for the audio, I have to assume that it's sending audio through BOTH the optical output and the HDMI output simultaneously. If the timing for the audio signal is slightly different, then that could cause the audio to be out of sync. Since the HDMI signal carries both audio and video, it makes sense that it would remain tightly in sync. But since the optical is separated it could, theoretically, not be synced with the video.
As I said, both of these AppleTV units have been hooked up the identical way that they are now and have never exhibited this problem until the 2.3/2.3.1 firmware updates.
I also noticed that unplugging the unit from power for 10 minutes, plugging it back in and testing the identical file that minutes earlier was out of sync, that the video and audio were much closer to being in sync. Does this make any sense?

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