2nd update. The factory reset worked.
However, I think the reason it worked is because it removed all the fonts I had added to the device. During my testing I made one change at a time and then tested the chapters and page jumping. It only broke again after I added my "Times New Roman" font to the device and selected it as my default font.
I'm not sure why this font is causing the page jumping or weird paging issues between chapters but if anyone else runs across this problem, I'd recommend changing the font back to the device default and see if that helps.
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