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Or maybe it's not so mysterious and I'm just overlooking something obvious...anyway. This'll be kinda long.
So here is the story. I had two creted geckos hatch three weeks ago today, on July 2. The first hatched at about 2:05P and the second around 8:30P. A few hours after they hatched and started wandering around the incubater independently and had recovered from the effort of the hatching process, I put them into the same tank for that night, a mid sized faunarium. I seperated them the next day because the first hatchling was twitching all over as if he didn't have enough calcium and knew I'd need to keep a close eye on him if he was going to make it, didn't prevent his tail from kinking up but he is doing fine now. The second hatchling is the one I cannot figure out why it died. It had been fine the first two and a half weeks then three days ago it slowed down from its normal self, so I kept up on his regular calcium/multivitamin regimine with a day of regular non-multivitamin enhanced baby food in between. No change for the better. Yesterday and the day before I noticed that he was really really plump. unusually plump. Almost swollen. It looked like he could pop. Now I knew I wasn't giving him that much baby food so I figured something was wrong but had no idea what. I looked around online called some people and nothing mocked these syptoms that I had seen. So then I thought hey maybe he's having trouble pooping because there didn't seem to be as much feces in his cage as there should be, I clean the cages once a week and there had been one terd for the whole week, so I got some warm-ish water and soaked his body in it for a few minutes and he didn't like that so he'd jump out. When I went to get him yesterday, he was very still until I picked him up. He then jerked a little bit and waddled around until I put him back in the cage. He died during the night and there was a bump in the middle of his head that was elevated higher than his eyelids. it seemed quite large and was almost mesa-like in appearance, the edges just dropped straight down instead of like a normal half-sphere bump. Does anyone know what may have caused this? The other baby is doing fine. Temps stay around 78 and none of the other cresteds I have in my room seem to be having any difficulties.

Could have been some sort of birth defect. Unless he accidently ingested some vermiculate from the incubation medium...that could cause the swelling your mentioned, and block up all his intestines so he couldn't pass. Really hard to say what happened, only a necropsy can indicate exactly what happened.
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PHLdyPayne