In complete work by builder for the apartment and cheque given.

Hello Sir, I booked an apartment with Tirumala constructions in Bangalore in the 2011 and after long delay the apartment was registered on May 31, 2014. Just before registration builder started forcing for payment of Rs. 1,35,000.00 towards services tax and then also assured to complete the pending work in 2 weeks. As work was incomplete even after 2 weeks i sent sms to builder to hold presentation of cheque. But on 17th June, 2014 builder presented the cheque without informing me and as it was my SB account the cheque returned due to insufficient funds. Based on the promise of the builder to complete the work i made a part payment of Rs. 50,000.00 on 24th July, 2014. But until now the work is not completed nor the service tax payment receipt issued. The cheque is dated 15th June, 2014 and its validity is expired now also i did not receive any letter or notice informing about the bounce and demanding the payment till now. The question is can the builder file case against me now under the NIAT for recovery of the balance amount. Will this have any bearing on the sale deed and property registered in my name. Please advice me on steps to be taken to protect myself from any further problems. Regards, Sanjaya