Hi Colin,
excuse me but I cannot reproduce your problem or I do not understand it really.

By the installation should be all three
page navigation active by default:
- for the 'overview' pages (main categories) on the top and at the bottom
- for the listed sub categories (on a category or sub category page) on the top
Also there is confusion between setting "Number of entries per Categories page *" and setting "Number of Subcategories"
The
categories page means only the
Startpage/Overview with the listed root categories.