I'm puzzled. The compatability mode change I've described does allow one to create table of contents and also (with editing of the opf file) to further incorporate the toc.ncx file to provide for the Kindle navigation. Originally I had the same problem with IE9 installed ie creating a TOC failed. At first I reverted to using IE8, then found this compatability mode information on the Microsoft site, tried it and it worked. I have used this to successfully create several books with TOC and the toc.ncx file as well.
I hope this clarifies things.