By default, Wayfinder orders the menu by the Menu Index number of each document (which you can change on the Create/edit Document screen), not by document ID.
If Wayfinder is ordering your documents by DocID (and you haven’t told it to do that with a parameter), it probably means you are using MySQL 5.0.51, which has a bug that causes that problem.
Some people have solved the problem by manually editing the Document ID numbers in the database, but that would make me nervous and would screw up any document groups you might have.
Another solution (what I’m doing for now) is to take out the "GROUP BY" clause in the SQL query in line 352 of the wayfinder.inc.php file in assets/snippets/wayfinder
$sql = "SELECT DISTINCT {$fields} FROM {$tblsc} sc LEFT JOIN {$tbldg} dg ON dg.document = sc.id WHERE sc.published=1 AND sc.deleted=0 AND ({$access}){$menuWhere} AND sc.id IN (".implode(',',$ids).") ORDER BY {$sort} {$this->_config['sortOrder']} {$sqlLimit};";
//took this out of above (came before order by): GROUP BY sc.id
This can create other problems, but seems to be working for me. I’ll change it back when the MySQL bug is fixed.
Of course the best solution is for you (or your hosting service) to upgrade or downgrade away from 5.0.51.
Hope this helps,
Bob