Even if you have a different header displayed on each page, by definition a [running] head is not on any page. As far as Word is concerned, a header is for multiple pages. Thus an Automatic TOC will not pick it up.

Move your tables from the header area into the body. Since they do not need to be running heads, there is no reason for them not to be in the body of the document.

Generating a Table of Contents - Complex Documents