The tables will not be created in Word to repeat but you should be able to apply that setting. You would have to do it table by table. Are you saying you have tried that and it will not work?
There is a macro on my site that is designed to apply various settings to each table in a document. You would need to edit it to do just that.
Word does not have an option to automatically apply it to all tables and it is not usually the default setting for new tables so I would guess the template has been modified.
See www.grainge.org for RoboHelp and Authoring tips
Actually the issue was there was an outline hidden box for each table. Hence, the Table Header was not getting applied. Removed the outline and applied Repeat Header Row.
The Header macro in your site helped to apply the Header for all the tables in the document.