I’m currently dealing with the consequences of the same problem. I paid tuitions to the university two months before my visa expiry date. Yet, university took 25 days to create my renewal account and another 50 days to submit docs and fees. My visa expired by then and I’m working on obtaining a special pass before getting the student pass now.
Unfortunately, there’s nothing you can do but keep pushing your university visa department or whoever handles your documents. And in case your visa expired during the process, you will be fined RM1,100 for the expiry. ONLY YOUR UNIVERSITY CAN HANDLE IT FOR YOU!