Maybe the Protomatter wasn't used in the cave? David said it was used to overcome certain problems, maybe those problems were of scale? The math likely said Carol's formula wouldn't be stable on a massive scale and David added the Protomatter, not knowing it would magnify the problem.
yeah, I doubt that protomatter was used in creating the cave. IIRC, the Genesis planet started to deteriorate rather rapidly. The cave seemed to be quite stable.