So what all do you think going into the founding of a new Chapter? I honestly doubt the Mechanicus just implants 1000 people and says "ok, pick a Chapter Master".
I personally imagine that experianced Marines from other Chapters, most likely Chapters that share a geneseed, to train the new Marines and probably hold the positions of Chapter Master and Company Captains temporaraly.
Hmmm, this could actually be an interesting Deathwatch assignment...