We changed to the Documentation theme and customized the navigation with the following:
{pagetree:sort=natural|excerpt=true|startDepth=3|searchBox=true}
However, the tree is showing twice. The first tree has startDepth 3 and then the search box and tree are shown again, although the tree is collapsed. Here is a screenshot of where the 1st tree ends and the search box and tree are repeated over again:
https://www.dropbox.com/s/yfcq6gpo6dt1aq0/Screenshot%202015-05-14%2011.14.23.png?dl=0
I had the same issue and un-checking "Page Tree" (this check box is above the Navigation configuration field) in the themes configuration resolved the issue.
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