Sam the mutt pup came to us as an about 9 week old with a raging case of giardia that took a while to correctly diagnose. Once the vet was on to it, Flagyl was prescribed. Most of the symptoms abated but it came back full strength after 8 days or so. Even though the SNAP was negative, I was sure it was still the giardia and urged the vet to prescribe something else. Did that, symptoms abated but it came back. A few days later, re-tried the SNAP and it came back positive. We danced this dance for 5 months. Finally, 3 SNAP tests in row came back negative and we were done with giardia. Poor Sam had a very sickly puppyhood. Giardia is very sneaky. I'm still crazed about the dogs drinking standing water outside. Our vet says that's where most dogs come in contact with it.
Hope your pup feels better soon!