yes. We think that the reason for the errors is because Moodle is loading all the courses and checking against the login user too.
We got a lot more courses in our system (over 4,100 courses) and 500 users. However, we do not enroll all the users to the courses. We are using guest access for all courses, and using enrollment for some specific courses (depends on the students' department) only.
We also tried to remove the navigation to all courses in the Navigation Block , remove the Courses Block , remove the Available Courses Block from Dashboard to see whether it will help speed up the login process. But no, we still faced the same errors as before.