Dog with Rabbit Yeast in Stool

Not knowing what specific tests your veterinarian has completed, it is difficult to say, but there are a couple of possibilities here...

1) Metronidazole (Flagyl) is a fantastic medication that covers a lot of different conditions... BUT, it is not 100% against all organisms. If you are having ongoing problems with loose stool, you may need to ask your vet to increase or lengthen the current regimen or change to a different medication.

2) Rabbit yeast may not be the primary cause of the loose stool. Many organisms that live in the bowel are "intermittent shedders" meaning that they produce identifiable structures such as cysts or ova only every couple to few weeks. It is possible that there are other organisms causing your problem, but that they did not show on a fecal exam, because they happened not to be shedding at that time. (Note: Flagyl is a treatment for many of these organisms, so it may be necessary to refer back to my first statement about resistance to Flagyl)

3) The loose stool may not be caused by any organisms at all... this may be an inflammatory condition. I'm not going to pretend to be an expert on the myriad conditions that could cause loose stool, but there's quite a few. Let your vet try medications first and rule out biological organisms as the cause first though... testing and treatment for inflammatory conditions is more invasive and less comfortable in many cases.

4) This could simply be a stress issue. Border collies and aussies are both known for being high-strung, nervous animals. Add to that the fact that you rescued, which implies a less-than-stellar personal history for your animal up to now, as well as the ordeal of Parvo that it has already been through, and you may be looking at a stress-caused diarrhea... it is caused by an overgrowth of certain bacteria in the bowel, and should be treated by the Flagyl... unless it is resistant (see item #1 again) or there is ongoing stress.

As far as the rabbit yeast, it is possible to pick up ANY organism if it happens to be on the grass... it takes your dog sniffing the grass in just the right place, and then licking their nose, and ~poof~... your dog has a parasitic, fungal, or bacterial infection. Just because your animal has no access to piles of rabbit feces doesn't mean that a rabbit didn't sit down for a second and rub its butt on the grass... that's all it takes.

Loose stool is a symptom of sooo many different conditions in dogs, it is nearly impossible to say ~this is the cause and the only cause right here~. Work with your vet, express your concerns, allow the medications to run their course before becoming concerned, and you will get the resolution you need.