Thanks for the responses. I am using hyperlinks for the cross references. The number in the text is set to jump to the beginning of the endnote line and the number at the beginning of the endnote line is set to jump back to the number in the text. As I said, it works correctly in the epub in Calibre, but when I convert it to Mobi, Kindle for Windows, Kindle Previewer on every device and Kindle app for Android all have the same problem. When you click on the hyperlink, it jumps past the destination by at least a line. And since it puts the line it jumps to at the top of the page, you have to page back to read what you jumped to read. Returning to the text is even more problematic because it reflows the text and when you then page back to try and find your place, it reflows the text again. It's very weird.
I just downloaded and tried the Mobi Reader and it does the same thing. Epub works, but obviously is not converting correctly to Mobi. I did try Zamzar, as well, and the Movi file converted there does the same thing.
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