If your chinchilla's stools are wet and mushy, then diarrhea is indicated. When your chinchilla comes up with diarrhea, there are a couple things you should do. Know your chinchilla's rhythms, and know if this is an indication of an ongoing problem.
Diarrhea can be a symptom of many things.
If this is an ongoing problem, then check with your vet, and do what you have been doing. If the diarrhea is a new condition, you should have your chinchilla checked by a vet, particularly a vet experienced with guinea pigs and other rodents. If they do, they need to be burred down - a procedure best done under anesthesia. If your animal has giardia, then ask for Albendozol, not Flagyl. Albendozol, however, usually does kill the bug after 3 days of treatment and does not seem to have bad side effects because it is not absorbed into the blood stream.