Hi Mary,
There is a difference. When you select a link from the navigation block it takes you to that topic but it is underneath the top topic area which, if full of information, means that you have to scroll down to the topic you have selected. It also hides all the other topics from view.
When you select a link from the section block then you are taken directly to that topic (no scrolling) and all the other topics are still in view, so you don't have click to unhide. It is quicker and more direct.
I have got my 'link course sections' ticked in Settings > Site Administration > Appearance > Navigation, but this does not make the links in the navigation block work the same as section links.
Chrissy