I think I get what you are saying. You are saying that when you get a variation of pheno's from one set of seeds, that the larger pheno's are often less potent than the smaller pheno's. That actually does make sense and I've seen this too but again, most often because you get a big pheno that is more Sativa like and starts to fox-tail. When it comes to plants that are more stable you won't see this happen as often. But yes I have noticed that sometimes the bigger plants don't seem as potent. The number one problem though is usually getting fox-tails or not letting that bigger bud actually finish up all the way. Selective harvesting is often used successfully for certain strains for this reason.
Quick question. Are you growing with American Genetics or European? I ask because that was something I noticed from European Strains back in the day, if they weren't stable hybrids the bigger pheno's were often more Sativa leaning and would fox-tail and take longer to mature fully.