I havent seen the car, cant say. BUT if your car runs well on petrol, then its only the 20K worth CNG kit that is making the problems
Why bullying the whole car for that.
And I am sure, if you visit a "proper" CNG mechanic, give him the correct problem statements, give him time analyze the overall CNG functionality in the machine, then it should not be a problem anymore.
Most probably, when the Advancer is not working properly while the car is running over CNG, the check engine light does get appear. Have you checked that, replacing with any other Advancer for trouble-shooting purposes...?
If you have been here in Karachi, I could have helped you better...