@fahadwizz
hmmmm... i think the blockage on the intake for cng is very less.try to block 50-60% on the air intake of ur car on cng (install the blockage after the airfilter, place scotch tape over the pipe) and then check it.on cng, the engine needs very less air to get to optimum burning.too much air wud turn the mixture lean and the car will not accelerate properly.
this seems to be possible because u said when u got the airfilter cleaned, car wasnt accelerating properly.
for my car, when i buy a new airfilter (obviously it increases the air flow into the engine) , the engine starts to drop rpms, then i slightly adjust the cng idle speed and gas inlet settings and it get back to normal.
@cool
i think ur problem can be same as this above one too!