The necropsy of one runt that I had (she lived to be 6 months of age and was no bigger than a one month old) came back showing a vitamin A defeciency....don't know why she was the only one that didn't grow or why she had a vitamin A deficiency when this runt and her siblings all got the same light, the same supplements, the same feeding, etc. I can only assume that some might have difficulty metabolizing nutrients for some reason.
This is something I wondered about with one of my runts. She seems to not store Vit A, even with a nice tummy on her. It just runs right through her, which means I constantly battle hypovitaminosis A with her. She has a larger runt sibling here, without an A issue. The other siblings here are huge and beautiful. At the time, I ruled out inadequate A as the cause of diminished size because 1. the very largest sibling here came down with hypo-A (did blood chem panel) at the same time as my runt showed the first symptom, thus it wasn't size limited; and 2. she was not growing from day one, and her hypo-A showed up almost 1 year later. One would expect (though we can be surprised!) that if she was more prone to hypo-A from the start, she would have at least shown symptoms, if not died, much sooner.
The slightly larger CB runt that has always, almost from hatching, shown a very unusual brilliant emerald color. She stood out from the other white-and-green striped babies, so I kept her. She is still this color, and is either UV-sensitive or temperature sensitive, she avoids prolonged direct sunlight and prefers dense foliage, like deep forest chameleon species. All the others, including hypo-A runt, are heavy baskers.
So the spectrum is: CB runt with hypo-A, slightly larger runt sibling without, some normal siblings without, and one big sibling with... plus 40+ sold siblings, only one I know of turned out to be a runt and developed hypo-A. The CBs, including my hypo-A runt, are about 20 months old. Both the WC and CB runts have juvenile color and features (neoteny) and look like 3-4 month olds. The WC runt is the same size as the hypo-A runt, and has been in captivity over one year. I'll wager he's about the same age as the CBs, as mine hatched at the same time this species hatches in Africa.
Does/did your runt have an unusual coloration or neoteny?
A blood test might tell you though. A vet might be able to do tests to determine a solution or at least a cause.
Some vets won't draw blood on a cham less than 12-14" total length, the caudal artery is too small. I had a vet who said the gauge required on a small cham would give poor results because the cells would get damaged. Necropsy is more likely, the vet can draw from the heart or aorta with a larger gauge needle.
It goes without saying that, as time has shown me that the runts have problems, they will not be bred. They are cute pets only.
Thank you for sharing, it gives us more pieces to the puzzle.