For all the presumptins regarding the NI please see the S.118 of the NI Act. The Cheque is not at all a promissory note. The act clearly says "s.4 promissory note, S.6 a cheque".
When a cheque is issued for making a payment of a particular debt, the fresh limiation starts, for this there should be a endorsement either in the cheque or in the promissory note.
The cheque is not an acknoledgment of a debt. It is only a discharge of a liablity. When there is a debt, the cheque can be issued. The cheque itself is not an acknowledgement.
The cheque as NI is valid for 3 years as per the limitation act. You can file a civil suit on the cheque within three years. But for a criminal liablity the cheque should be presented within 6 months. In case of a cheque bounce, you can file a civil case as well as criminal case.