One week ago, This issue was elevated to the adobe Indesign level 2 team.
You need to check "Make text anchor in source paragraph" on the Table of Contents Options.
Thanks Ellis. Sorry about the later response. I did that. I am still unable to get the TOC to be set up the way I want to. Adobe Technical support has still not sorted it out.
I would need more details from you. Which version of InDesign are you using? Have you tried opening the same EPUB in any other reader like Readium or iBooks? If yes, is the behavior same in these readers or different?
Since I am not able to reproduce this issue at my end, test files (InDesign documents as well as the EPUB) would be helpful. Would it be possible for you to share them with us? You can upload the files to drop box and share the link with me. (email: firstname.lastname@example.org)
Actually, inDesign Tech Team level 2 is working on this issue.
It is late here so I will get them to you in the morning. Again, thanks.