Maybe she also has a gastric ulcer along with the giardia? (ulcers seem to be pretty common in ferrets). I didn't see that your vet had prescribed anything for that. The other thing that ferrets get commonly is ECE.
Here is some info on ulcers:
GASTRIC ULCERS : A "Hole" Lotta Trouble by Dr Bruce Williams
( Ferrets Magazine March/April 2004 p. 18 - 23)
Why are gastrics ulcers so important ?
3 reasons : they are common, they are often overlooked and
they can de deadly if ignored.
3 visible signs that should not be ignored are :
Bruxism ( a sure sign of abdominal pain)
The passage of thick, black, tarry stools
or the presence of this type of material around the anus.
OK his treatment for ulcers :
Filling the ulcers : My preference is to fill those ulcers.
I always have liked the analogy of ulcers as potholes, and
sucralfate (also known as Carafate) is a wonderful drug to fill them.
It adheres only to ulcerated mucosa and acts as a tempory patch,
preventing the acid from hitting the tender tissues.
The secret to using sulcrafate (which many vets may not know)
is the timing of each dose. It doesn't hang around long,
so it needs to be given 10 minutes prior to each meal.
Ferrets don't secrete appreciable amounts of acid between meals,
so the typical 8- or 12 hour dosage regimen often used with dogs
generally doesn't work. I patch those holes with a dosage before
every meal, no matter how often I feed the ferret.
Bland diet : Ferrets with ulcers don't digest anything well and they
often don't eat much, so they need to get as many nutrients as possible
out of each meal. Kibble is not easy for these animals to digest or
absorb, so I withhold it for at least 30 days (and gradually reintroduce
it when I am confident that the ulcers have healed). I prefer a highly
digestible, semisolid diet. I'm a chicken baby food advocate, but other
for of bland diet such as
duck soup or Hill's a/d prescription will work.
The key to a bland diet is to offer it frequently (every 3-4 hours)
and in small amounts (and don't forget that sucralfate 10 minutes prior
to each meal !).
Importance of water : Ferrets with severe ulcers or those that refuse
food may suffer from dehydration. Offer water by hand to these animals
often.
Minimize Stress : A phenomenally important but often-overlooked facet
of ulcer therapy is minimizing stress. Many ferrets develop multiple
problems and, while it may be convenient to treat for several at once,
the stress of medicating ferrets every couples of hours may worsen
many cases. For example, I have discontinued the practice of treating
ulcer ferrets for Helicobactor, as the stress of medicating for both ailments
usually out-weighs the benefits of therapy. Helicobacter is a chronic disease
that doesn't kill ferrets ; generally you can wait a couple of weeks before
treating even the most severe cases.
I often am called to consult on ferrets with obvious ulcer disease that
are on multiple antibiotics, acid blockers, prednisone and even more
drugs for other conditions. I such cases, the first step to recovery is
removing each medication that is not absolutely necessary at the moment.
Dr Bruce Williams, DMV, DACVP
and here is a link to ECE:
Epizootic Catarrhal Enteritis (ECE)
After several trips to three different vets over the course of a year, we finally proved she has the nasty parasites (Giardia). She was prescribed Metronidazole for 10 days, and for several months we thought she was cured..... Until two nights ago. At 12:30 AM early Wednesday morning, my husband started yelling for me. Sammy (My 2 year old spayed female was heaving trying to vomit, and bleeding diarrhea from her other end. One look at the blood and we were on our way to our local 24hour 
Samantha
R.I.P. Ginger "you were the best dog ever!"
Tink can fix Anything!
I have been sent a Valentine 
