Interesting problem that I just resolved with the Cineform folks. We use the stand alone version of Connect HD. I was experiencing audio synch problems when I converted to the CF AVI and chose not to use scene detection (we prefer to capture entire tapes). The m2t was in synch, but my avi's would be off up to 30 frames, actually the audio was shorter than the video. If I encoded using scene selection, all was well. I couldn't figure this out, but was really getting frustrated. I racked my brain for a cause... I captured a continuous run of 20 some minutes with no problem. Then I attempted a tape that had several start/stops in it and the problem returned. I told CF support that I used the "quick record" mode on my Z1as we didn't like to wait for record to engage when it has set a little while. The manual indicates that the camera may record a few black frames in this mode. This is the cause of the problems. Here is a part of the response from CF. They were very helpful.
"That makes perfect sense, and it also explains why using scene detection remedies the problem. I'd imagine that the synch is off by as many frames as there are black frames in the stream.
The way Sony does scene split (with quick record OFF) is quasi-intelligent, cueing to the correct end marker left with the previous scene, and will result in that smooth transition between scenes. Quick record ignores this and will just start to write to tape when record is pressed, thus creating a "black frame" which is technically MPEG stream corruption. Our scene detection algorithm picks up on this and breaks in the appropriate location, resulting in properly synch'd audio.
So, that leaves you the option to either capture with scene detection on, or shoot without "quick record."
Thank you very much for bringing this to our attention"

Tim at Cineform was quick to respond. It's nice to work with a company that supports its users.