Trouble publishing ditamap with topicrefs.

I have a ditamap that contains some topicrefs and some dita files. When I use 'Save DITAMAP as...' Book 2017 with fm components, the book does not publish as I would expect. The chapter hierarchy is messed up.

DITAMAP structure (using numbers to show hierarchy):

1 Intro

2 Setup

  2.1 Roles

  2.2 Permissions

  2.3 Authorization

3 Real-Time

4 (topicref with navtitle "Configuration")

  4.1 Source

  4.2 System

  4.3 Reports

    4.3.1 Report A

    4.3.2 Report B

Generated TOC:

1 Intro

2 Setup

3 Roles

4 Permissions

5 Authorization

6 Real-Time

MISSING (topicref with navtitle "Configuration")

7 Source

8 System

9 Reports

  9.1 Report A

  9.2 Report B

Any ideas what might be causing this?

Thanks!