Last modified: 2013-01-30 16:38:09 UTC
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).
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 :)
Here you go https://gerrit.wikimedia.org/r/#/c/42588/ :)