think about it. the mib was knocked unconsious by whatever he hit his head on, and probably dies as soon as he hit the ground, jack on the other hand took a little bit of time to pass away. maybe in order to become the smoke monster your mortal body needs to be dead. as soon as jack's body died, a smoke monster came out of the source. and maybe this time, jack decided to help hurley and ben protect the source. and this smoke monster became what rousseau said the 1st one was a "security system" jack protects the source and smokes out every time somebody gets a little too close to the source.