Dear Sathish, 

There is a mistake here, the MBBS seats in Sri Ramchandra Medical College, Chennai, are not allotted under All India Quota (AIQ), rather it is a Deemed University and thus admissions in it is done by DGHS, which is also a counselling authority for AIQ admission, but the counselling for Deemed and Central Universities are separately conducted by it under separate banner. 

Now coming to your question as to why some seats might have remained vacant. It might often happen that a student is offered an MBBS seat during NEET counselling, but the seat is rejected by the student, eventually resulting in a vacancy. This could happen for a variety of reasons, like relocation issues, lifestyle problems, incompatibility with the state in which admission is being offered and fees, whic is one of the biggest of all. 

Sri Ramchandra Medical College is one of the best Deemed Universities in India, with it scoring 183.5 of 500 in Careers360 ranking parameters and getting a rate of AAAA, which corresponds to 'Very Good'. The reason as to why students rejected a seat here might lie in its fee structure. It has one of the highest fee structure for MBBS seats in India with one management seat costing INR 22 Lakhs per annum, the same for NRI seats is 2,20,000 USD. 

As per the counselling procedure, all the seats which remain vacant after Mop-Up round in Deemed/Central Counselling, they are sent back to the respective university or institutes and they take admission on those seats under state counselling.

Hope it answers.