To reproduce:

1. Use a user and site with overdue events on timeline.
2. Select All filter in time selector.
3. When changing from Sort by dates to sort by courses overdue events are not shown.
4. Now change to Overdue and back to All filter.
5. As you can see, there is a different output will be shown from step 2. Now overdue events are shown and this is correct.
6. Also the order of the courses should be checked. In the WS get_calendar_action_events_by_courses courses are sorted in enrol_get_my_courses using $CFG->navsortmycoursessort.