Is there any Check Engine Light visible?? If yes, then get it scanned and post the DTC
If the car is on CNG, it is most likely the Advancer. I am not saying it is faulty, you just need to identify the problem by disconnecting all Advancer/Emulator wiring and bring back your injector and ignition wiring to stock. Would hardly take 15 minutes at home. Start the car and then check.
In theory, if your problem is resolved now, its either the advancer or any wires going to advancer.
If your problem still persists, the check engine light should glow on.
Below pics might help in bypassing the emulator/advancer