hmm.. i probably wasted atleast 5 hours trying to figure this out in the past few months. Now i have it; noting so i have it if i forget again.
To correctly number new sections in a word doc:
1. First type in text
2. Select text and select the proper heading style (Heading1, Heading2 etc) - no numbers yet
3. Select the text and click on "Multilevel list" short cut and select the type (1, 1.1, 1.1.1 in my case) - it will give it an incorrect number if the paragraph is nested; the most difficult part is next..
4. First select the number (not text; select the number given) and right click select continue numbering - still not the right indent level
5. Select the number again and click on "Increase Indent" button until i get the right indentation level.
hmmmmmmmmmmm.. done.