Update: I am back to 100% enrollment after bulldozing the one Dormitory at my University. I recommend just using the Dormitories to level up the University and then removing them after that.
I have a similar problem. 9100 students in my city. I have 3 universities one at level 5, yet I only get about 4800 students enrolled everyday.
So I started a new region. I built a city that started out fine with huge enrolment. Now the city has 2650 students but only between 350 and 650 students will attend school. I have a level 3 university and an upgraded elementary school. The purple bars on the education overlay show that I only have 17 students not attending. All the rest of the residential buildings have green bars or no bars at all. My city is slowly going abandoned because of no schools. There are no traffic problems at all and no traffic building up on the highways leading into the city.
Also in this second city I have 1150 students commuting in from other cities according to the reports, however my university shows that it only educated less than 450 students today and my elementary school educated 214 students. The numbers do not add up!
