Dear Raj, You have to check with your Pay Roll office on this first about the discrepancy.
You can withdraw EPS amount only when you are withdrawing EPF amount and that too if you have not completed ten years of service. If you have completed ten years of service then there is no way to withdraw your EPS amount. You will receive a Pension Scheme certificate for the EPS amount.
You can withdraw the contributed EPS amount along with your EPF balance. But the condition is you must not have completed 10 Yrs of service. When you withdraw EPF, then you receive EMPLOYEE+EMPLOYER EPF contribution+Interest earned on this EPF. Along with that, some % of EPS contribution also be paid.
You'll know some more details about the EPS from the attachment.