Is seems that some enrolment plugins cause users to be automatically unenroled from invisible courses when they login. And that seems to be far from correct.

IMO visible/invisible status has NOTHING to do with enrolments (just the role/caps/perms system will grant users can/cannot access to the course).

So it would be interesting to iterate over all enrolment plugins, checking that $course->visible doesn't cause the unenrolment any more.

Just some hours ago, it was fixed in the LDAP enrol plugin from 18_STABLE to HEAD.