Sometimes puppies with negative fecal tests have false negatives -- giardia is very hard to spot on a fecal float (there's a special test for it, but many vets don't stock it).
We just had a 14 week old pup in foster care with persistently returning "pudding poop" that got better, then cycled back. The fecal float was negative, but the vet suspected giardia or something weird requiring a special lab test to diagnose. Before spending $150 on an IDEXX lab test for a huge range of different bugs, I asked to treat as though it were giardia: we did a full week of Panacur. That fixed it!
Panacur isn't expensive. It's got a broad safety profile. I would ask the vet about trying it -- I wouldn't do less than 5 days of it, and I really think 7 days makes a difference (that's longer than typically prescribed).