Sorry, I had meant to reply earlier, unfortunately I didn't have much to say.
Yes, it looks like it is crashing in an area of the code that deals with hyperlinks/crossreferences.
That is unfortunately not a surprise
Thanks, John. I appreciate any response. Like I said above, I've created this goofy way of making endnotes that works for now. I've alerted the proofreaders that I'm doing the notes essentially by hand, so this job is fine. But I can not do this forever. I've kept CS5.5 on my machine just in case, and I'll file a case.
Thanks again, and tell someone at Adobe that this is serious!
Also, we need automatic endnotes.
I was just doing some searching to see if they fixed the cross references problems in CS6. Sounds like not. I've been using this third-party plugin recommended by others. It's not cheap, but the customer service is quick to respond. And they have free upgrades when a new version of InDesign is released.