The "Courses" link in the personal tools, which links to Special:MyCourses, only appears if explicitly enabled in Preferences > Misc.
It should appear by default for any user who has a role in a Current or Planned course (whether instructor, campus or online volunteer, or student).
Version: master
Severity: enhancement
The behaviour you describe is implemented, and seems to be working (I just tested locally). Please reopen if it's really broken.
I had thought this was working as well before, but an instructor reported that it was not showing up on English Wikipedia for her (eve though she had created a course page and signed up as the instructor).
I tested it on test2 by resetting my preferences to defaults, which made the Courses link disappear on an account associated with active courses.
And I just confirmed it on test2 using an account that previously hadn't done anything with the extension. Neither signing up as an instructor in an existing course, nor creating a new course, made the Courses link appear.
Oh wait... this only works when you enroll as a student. I'll add in this behaviour for other types of enrollment as well :)