Any other symptoms? If they weren't moving, I'm not totally convinced that they are parasites, but anything is possible!
Runny, smelly poo can come from many different problems due to the digestive system. Many parasite treatments are NOT specific to any one bacteria or other microbes. Often it is similar to something like a "colon cleanse" and just wipes everything out. It's important to monitor (like you're doing) for a few days to ensure that the regular intestinal microflora can resume its lovely existence in the GI tract. I would venture to say that if the cells can not be identified, that the runny poo may be the result of a stressed and very "clean" set of intestines.
Unfortunately, I'm not 100% sure of a treatment in chameleons for inducing pre- and probiotic growth.
Let me know if the little buggers were swimming or just hanging out. And when your vet gets back to you, let us know about that too!
Good luck!