Change the setup of your lists. Numbering in Word is broken unless you handle it very carefully.

How to create numbered headings or outline numbering in Word 2003 and earlier versions

That link currently is not working. It will be again soon I am told. I recommend trying until you get the page because it has very clear instructions.

In the meantime, take a look at:
Numbering in Microsoft Word
Word's Numbering Explained by John McGhie, MVP
and How to Create a Template. That last one has a downloadable template that has solid style-based numbering built into it.