Trying to avoid the scroll of death, I used section 0 as a menu: it contains links to all sections. Then, I modified the number of topics in the course settings to "0", so all the other sections are "hidden".
)A better explanation here: https://www.youtube.com/watch?feature=player_embedded&v=XtHPUh_BaxM).

Once the section is "hidden", the checklist (which supposed to contain the resources and activities from the current section) is empty.
When I set the number of topics back to 40, the checklist is fine and all the items are there.

The same happens with the Subpage plugin (here: https://github.com/moodleou/moodle-mod_subpage).
I added a subpage resource to a section and a checklist activity to the sub-section. The checklist is empty.

I believe the two are symptoms of just one problem, because the subpage is actually creating "hidden" sections and present those sections on a different page (the subpage), so it seems like sub-sections. While a section is "hidden", its resources and activities are "orphans". Even though there is a deferent "orphan section" to each "hidden" section, the checklist is unable to show the related activities.