Ok. So 25 clutches all in all and 7 of these clutches were of the darker type. It sounds logical that your male and one of the females produce the darker neonates as cdmay and n2torts suggested.The first year I found the first one was all alone, then the same year I found three from one clutch (all hiding at the same spot) as they all hatched at the same time. Last year I found two + two, and one single one, and this year I would bet that even if I found one dark all alone first and then the slightly brighter one, the first dark one this year belonged to the same clutch I found when emptying the enclosure with two more dark ones. So all in all my best guess is that these 13 hatchlings (I've checked my logbook now) comes from 7 different clutches. And during the three years these three females in this group has laid 25 clutches in total (those found included). All with the same male but three different females.
The only thing is, its a mighty coincidence that all the clutches left in the ground ended up the darker type and from one female.
Also do you know if you have definitely incubated eggs from all 3 females artificially. All your artificial eggs were of the brighter colours, yes.
It's very interesting either way.