The standard Nonzero theme makes makes all items in a course section invisible in two situations:

1) when the weekly format is being used and the secton is the crrent week, all items are invisible

2) when the topic format is being used and the section is highlighted as the current topic (i.e. the light bulb is clicked on)

This does not happen with the standard theme, but may happen with other 'default' pre-installed modules

This may be connected to MDL-27160

And finally, a plea from an overworked Moodle admin: please please can features that worked and were standard in Moodle 1.9 be made to be present and functional in version 2. Thanks.