I havn't heard of this issue before I'm afraid. It's hard to see if they are not open as master pages etc somewhere else in the application without seeing it.
I guess if you can preflight it you must have an epub exported if its the html toc not showing it is probably an issue with the html.
I can generate an html contents page for you if you have the toc.ncx file?
Feel free to email me ed at stunjelly.com
ebook formatting and repairs