This issue was discovered while pre-testing MDL-57564 and also noticed by dougiamas as affecting one of our HQ internal sites. I was originally trying to cover it in MDL-57564 but haven't find a trivial way to do it.

Steps to reproduce

1. Set $CFG->navsortmycoursessort = 'shortname';
2. Set $CFG->navshowmycoursecategories = 1;
3. Prepare a structure of course categories with subcategories
4. Put courses into these categories, named randomly
5. Enrol a student into all these courses
6. Log in as that student
7. In the Clean theme, the My courses will be displayed as a tree of categories - with courses within each category sorted per the configured field (such as shortname).
8. But in the Boost's flat navigation, the categories are not displayed. So only the courses are projected into the flat navigation.

• Expected behaviour: The courses should be still displayed ordered by shortname even in Boost
• Actual behaviour: The courses are displayed in the order given by the categories tree

The problem is illustrated in the following screenshots that show the same site in both themes: