In order for Acrobat to recognize the table of contents (TOC) in a word document – the TOC must be based on Styles. If the TOC format has been altered (no longer based on a default style) then the conversion won’t pick it up.
Is your TOC being created in Word using the Insert Index and Table Reference command, or manually created?
If you are using the Insert TOC:
In the TOC dialog box in Word – you can click on the options button to set additional formats you want it to pick up. You can click on the Modify button to change the appearance of the text in the TOC. Make sure this window shows all of the styles you are using in your document.
If you manually created the TOC:
You need use a style in the formatting of the TOC. You can use any of the built in styles or create your own. Once you have done so, you need to change the setting in the AdobePDF menu to pick up the style you used. Adobe PDF, Change Conversion Settings, Bookmarks. Click any style you used. Notice at the bottom of the window all of the TOC styles are checked by default, so using the insert menu will automatically pick them up.
Hope this helps.
Samaba