I got an official reply from CPC Commissioner on the grievance I raised. I was told to go for rectification. It's a bit surprising that members here are recommending for revised return. I meant no offense to anyone, but for income tax matters always cross verify things a few times. Looks to me like most seasoned experts in this matter may not be aware of all the proceeding. Just my two cents.
Here is the reply from CPC -
Resolution: Dear Taxpayer, payment details of Self Assessment Tax was not entered in Schedule IT or TAX PAYMENT while filing the return. Request you to fill the same, PLEASE RE-ENTER DETAILS OF ALL CREDIT IN SCHEDULE. IT OR TAX PAYMENTS, INCLUDING ENTRIES MENTIONED IN THE ITR FILED EARLIER, SO AS TO GET FULL CREDIT and file online rectification by logging on to http://www.incometaxindiaefiling.gov.in. For further information, please Go to "Help tab"-> " Filing of Income Tax Returns and Forms"->"Rectification of ITR". If you are still not able to file online rectification, kindly contact E-filing Help desk on 18001030025 or 8046122000.