We've created this Forum Thread with some workarounds and advice to assist you in publishing you ebook.
TOC not fully coverting
I have very carefully marked all my chapter headings Header 2. After I convert the file, it says I have successfully converted to E-Pub, BUT not all of my chapters are appearing in the TOC. Any suggestions? (I have revealed codes in MS word and I do not see any unusual spaces or codes or characters).