Well i don't know about the Karachi workshops as I am I live in Lahore..
First of all you must start your car on petrol and then it will auto switch to cng.. it will be good for your car engine life and performance.. Get your cng converter checked..
Secondly as you use to start car on CNG, get your CNG kit tuned for starting problem..
Thirdly do over all engine check up, like plugs, throttle body etc.. Go visit a authorized Hyundai Mechanic..
It seems your car is being not maintained and require proper tune up only..