There's another probiotic that a member here suggested when Gabby was having problems with diarrhea --
Renew Ultimate Critical Care. It has a high percent of bifidobacteria -- much higher than in FortiFlora. I found it in the refrigerated supplement section at Whole Foods.
Did you try metronidazole (Flagyl)? Gabby went through 3 bouts of vomiting and liquipoo not all that long ago. It took about 4 - 6 weeks on the meds for her system to get back on line. My vet tried a shorter course and whatever was going on came back. The only thing that we also did as a last resort was a fecal culture. It's a test that Idexx labs will run and it's not cheap. It will tell you if there's anything bacterial growing. If you look on the "lab results" tab on Gabby's SS, at the bottom is what the culture assay for. Did the vet also rule out giardia?