Pyometria is only in unspayed dogs(female). It is an absolutly massive in ifection that can sometimes not even show up in bloodwork. I would also be concerned with the vet throwing antibiotics at this except one thing he saved Clavamox for backup. Yes it can be very expensive in these large dogs but it is a great antibiotic. The vet throwing out these other possible diagnosis is not necessarily incompetance, as much an expression of fustration at not knowing everything.
A few things if this persists, they really, really need a sample, you need to bring her back, and when you do consider asking them to take an abdominal xray. If you have to call for an appointment ask if your favorite vet can consult with this one you dislike, but try to keep the one you dislike as they know the case history and won't be going strictly off the patient notes and this case seams to be a learning experience for him?, don't take away the final. Good luck keep us updated. Tim