Try this:
1. Open your project.
2. Click the Project tab.
3. Right-click the Single Source Layouts folder and select
New Layout. The New Layout dialog will appear.
4. Enter a name for the new layout in the field provided.
5. Select Printed Documentation from the Output Type
drop-down menu.
6. Click the OK button to close the New Layout dialog. The
new output will be listed in the Single Source Layouts folder, and
the Print Document dialog will appear.
7. Click the Next button.
8. Delete everything from the Chapter Content display window.
9. Click once on the desired chapter in the Topics display
window.
10. Click the > button.
11. Save the layout.
12. Generate the output.
I can't be sure, but I'd guess that you added these topics to
your TOC but didn't update your Printed Documentation layout. This
layout matches your project's TOC when you first open/save it, but
it doesn't automatically update itself after that; you have to add
new topics manually.
Try that and let us know how you get on. Good luck!