I got something strange for you:
I created an eBook in InDesign CS 5.5 and I am content with the results in ePub
I converted the ePub file via calibre to .mobi and put the book on my Kindle.
What did I see?
The table of content is at the END of my book, instead at the beginning.
It functions just fine, you can use the chapter links and you can definitely choose "Menu > Go to > table of contents" in your Kindle.
But why is it at the very last page?
Maybe someone has an idea to fix this.