Are they from Female? I just finished a run of Female Ak and Female Auto bubble. They were all different phenos. 1 of the AK was a Hermie and I ended up getting seeds out of both strains. I almost threw 1 of the Ak and 1 of the Bubbles away cause they just didn't grow right. The bubble I was gonna pitch ended up yielding over a qp dry of shit IMO. I ended up just making bubble hash out of it. The AK's ended up above average but the bubbles suck. I grew mine in coco so I can't be much help with your system but I can tell you that I had some similar experiences. My best AK started as the runt but finished strong. What is your ph?
I must admit that after this past run of auto's I can say I am over them. It's easier, just as fast, cheaper and I yield more from clones.