It is a really complex rendering. But I can let it sit for a minute or two, giving it all all the time it needs to sort things out, and it still behaves the same way: it all starts playing just fine, then a few seconds later, most if not all pre-rendered tracks just mute out, while Audition plays on.
I couldn't manage to figure out how to record the audio, but I did make this little video of my monster session, pre-rendering the tracks and playing back.
Pre-render Woes - YouTube
I pre-render every track, then hit play at around the 1-minute mark. You can see it's playing back by watching the meters in the lower left. And then most of it cuts out. The only thing left playing is one track I couldn't pre-render because the effect is on a bus track. But you can see how must of the volume drops out.
Is there anything else I can tell you? I appreciate your help!
Update: After trying so many things, I think I found a solution to this problem, even though it sounds to me like a far-fetched connection. I updated my system's BIOS. Lo and behold, Pre-render worked again. I have no other way to explain it, but that seems to have done the trick!