Why are courses missing from My courses ?
Perhaps you have hidden them in your Dashboard. See How can I remove a course from the list of My courses? in this FAQ.
If so, you'll be able to see them if you click on List all my courses in the Administration block on the frontpage of Moodle.
Otherwise, you are not enrolled to the courses.
This is probably because you are not registered to them through through Minhal Talmidim.
Note: During the first four weeks of the semester, you can enrol yourself to most courses.
However, unless you are registered through Minhal Talmidim by the end of the fourth week, you will automatically be unenrolled.