I dont think what you mention is knocking. Knocking is due to detonation in the combustion chamber and MJDs dont knock whatsoever. If you leave the accelerator and there is sudden drop in rpm or some jerk the very first thing you should do is clean the air filter. Better replace if too dirty. Secondly check each and every turbo hose and mainly the air intake hose that is hooked to the bumper from the engine cover/ airbox cover. Since your is a 90 BHP punto with VGT make sure the Vacuum Solenoid plunger that activates the Turbo Vanes is moving up and down. In your case in am suspecting some turbo hose leakage due to the symptoms you are facing.