I load a doc.x file into Calibre. The file has a hyperlinked table of contents which works perfectly well in the doc.x file. I convert the doc.x file to the MOBI (or EPUB) format. I can see the table of contents in the MOBI (or EPUB) file. When I click on any entry in the table of contents Calibre takes me to the first page of my document. It does not take me to the chapter start page.
NOTE: A year or two ago I used to use MobiPocket Creator to convert my doc file to HTML. I added 'hooks' to the file while it was resident in MobiPocket. Next, I opened the HTML file in SIGIL. IN SIGIL I worked my way through the file, highlighting all the chapter headings and assigning H2 header categories to each chapter heading. Last I pushed the button to generate a table of contents. Moments later I had an EPUB file which Calibre converted to the MOBI format with a working table of contents. I was able to upload these files to Amazon, so I knew I was doing things right. What pray tell, am I doing wrong this year?