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@Jim: Yeah, I've looked at it both ways on the Nook Color and it's an issue both ways.
@eping: I hadn't thought about it being an overflow issue, but that makes sense. After a lot of digging around a co-worker found out that it's actually an issue with Adobe's reader on the Nook Color. I've actually resorted to what you said, but I re-exported the endnotes from InDesign as a paragraph style and then cut and paste the endnotes from that epub file into the one I had already spent time on fixing.
The real downside is that I had finally gotten a neat little javascript to that would connect the static endnote reference numbers to their corresponding endnote in the back, but for the script to work it needs to be turned into an automated number list. That was really sweet, but Nook Color has rendered that useless and now I need to rely on running GREP in Sigil in order to do this, which has it's quirks. I swear, every time I think I got this epub stuff down some company throws a monkey wrench into my work flow and I've got to rethink everything. It's like Beta vs. VHS on meth.
Thanks for your replies.
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