Even when bypassing splitters altogether and using M2TS with h.264/AC-3:DD5.1 (per ceton) nearly all of my 1080p rips will hit a particularly "difficult" scene (high detail, high motion) and the audio stuttering and macro blocking will begin, and from that point on it won't recover. (pausing, FF, skip forward.... nothing will get it back to a watchable state)
What this tells looks like to me is WMC is delivering the audio and video streams to the extender just fine, (since they will often play an hour or more before displaying the above behavior) so the problem either lies with the networking subsystem being able to deliver the peak bitrate scenes or that the video subsystem is unable to process them. Intuitively I would think a network problem would be easier to recover from, which makes me think it is a problem with decoding the video.
Considering the history of the echo to this point in regards to live video, I'm inclined to point at the video processor and say it is the problem. I'm still optimistic that Ceton will get it ironed out, but I'm hoping I don't have to remux all of my videos.
RAID protection is only for failed drives. That's it. It's no replacement for a proper backup.