OK. I've uploaded a zip file that contains a sample epub and the Mobi file that Calibre produces. The epub endnote references work like they should for me, but in the Mobi file, clicking on an endnote reference takes you to the line after the destination and clicking on the endnote number takes you to the beginning of the paragraph after the paragraph containing the destination reference. This is a very small portion of my client's copyrighted book. Please use it only for troubleshooting the reference issue. Thanks for your help.
SampleEbook