Hi Kris,
I've recently went through something very, very similar with a couple of my animals.. (more like 15). At first, I thought that I was being plagued by crypto as well. All my animals were showing the signs (everything but the cottage-cheesy stools), dark runny stools with a very sour smell, lethargy, and with some of them death. I took the animals with stool samples to several vets, and crypto wasn't found. I even had them perform a necropsy on one of them that passed away. Expensive procedure, but well worth it. Crypto wasn't found in any of the tests (tissure or fecal wise). After trying Panacur and flagyl, my vet told me to try Sulfadimethoxine (generic - Albon). And this actually worked within two treatments all of my babies and some of the infected adults started to show signs of improvement. I'm kinda thinking that it was a coccida-like protozoan that was infecting and devastating my colony. But it wasn't crypto. As far as the black stomach goes, well that could just be feces inside the babies gut. You can actually see the poo inside the little animals (I think this is because the skin on the tummy is so thin at first), then when they go poop the dark spot is gone. BUT I've seen animals infected with all kinds of parasites (worms, trichomonas, coccidia) that exhibited the dark blotches on the stomach, though in my experience these blotches were more a blue-green color outlined in a bright red. May just be me, but this is what I've seen. If those were my geckos I'd take'em to a vet ASAP... Who knows, maybe it'll be treatable... I'd wait to blame the problems on Crypto until all other avenues have been checked (bacterial and such). Hope this helped, and good luck.
Richie