I've found the same thing too. The quicknav seems to work on pages at the same level.

So if you have only pages and no sub-menus it works as expected.Or if you have pages all at the same level of sub-menu it traverses between them all too.

There is a branch of the plug-in on github that provides a fix.

This branch in my testing places the quicknav on all pages as expected but seems traverse between submenus but only up. So with structure:

Page 1

Section 1 - page 2

Section 2 - page 3

Page 4

The Quicknav next button goes from Page 1 -> Page 2 -> Page 3 then cycles between Page 2 and Page 3

But, you can use the global manual setting in contentObjects.json to get from page 3 to page 4: eg

 "_global": { //change the flow for global continuous
        "_pageNext":"co-10", // remove if to follow normal flow set to id of page 4 in our example
        "_pagePrevious": "co-10" // remove if to follow normal flow
},

But, i don't think these options are available in the authoring tool.

Hope this helps

Joe